<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2026 Workiva-->
<!--r:019e2cc3-ec99-7c25-967a-13541cadc0d6,g:cb5c0ecf-126e-4d6f-852f-6744cec6ceeb-->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:arcroleRef arcroleURI="https://xbrl.org/2023/arcrole/summation-item" xlink:type="simple" xlink:href="https://www.xbrl.org/2023/calculation-1.1.xsd#summation-item"/>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/CondensedConsolidatedBalanceSheets" xlink:type="simple" xlink:href="pcvx-20260630.xsd#CondensedConsolidatedBalanceSheets"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/CondensedConsolidatedBalanceSheets" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-7480-9111-4c36faeae3ab" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PreferredStockValue_019e2cc3-ed5f-7f80-a9a1-e278b973e8c2" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PreferredStockValue"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-7480-9111-4c36faeae3ab" xlink:to="loc_us-gaap_PreferredStockValue_019e2cc3-ed5f-7f80-a9a1-e278b973e8c2" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommonStockValue_019e2cc3-ed5f-7eea-bd1e-4141332c5fdf" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommonStockValue"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-7480-9111-4c36faeae3ab" xlink:to="loc_us-gaap_CommonStockValue_019e2cc3-ed5f-7eea-bd1e-4141332c5fdf" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AdditionalPaidInCapitalCommonStock_019e2cc3-ed5f-722a-8699-1a75f6b92b65" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AdditionalPaidInCapitalCommonStock"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-7480-9111-4c36faeae3ab" xlink:to="loc_us-gaap_AdditionalPaidInCapitalCommonStock_019e2cc3-ed5f-722a-8699-1a75f6b92b65" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax_019e2cc3-ed5f-7cdc-9724-9f498f222b14" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-7480-9111-4c36faeae3ab" xlink:to="loc_us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax_019e2cc3-ed5f-7cdc-9724-9f498f222b14" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RetainedEarningsAccumulatedDeficit_019e2cc3-ed5f-7ffe-9807-d004c0d1e2bc" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-7480-9111-4c36faeae3ab" xlink:to="loc_us-gaap_RetainedEarningsAccumulatedDeficit_019e2cc3-ed5f-7ffe-9807-d004c0d1e2bc" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_Assets_019e2cc3-ed5f-7b67-93fa-4cd2b6987317" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Assets"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AssetsCurrent_019e2cc3-ed5f-7471-b856-058f1d8681c6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsCurrent"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_Assets_019e2cc3-ed5f-7b67-93fa-4cd2b6987317" xlink:to="loc_us-gaap_AssetsCurrent_019e2cc3-ed5f-7471-b856-058f1d8681c6" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-7ed3-9169-1e891b4c24c3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsNoncurrent"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_Assets_019e2cc3-ed5f-7b67-93fa-4cd2b6987317" xlink:to="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-7ed3-9169-1e891b4c24c3" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LiabilitiesAndStockholdersEquity_019e2cc3-ed5f-78e9-b25b-12fdf2334a3e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesAndStockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_Liabilities_019e2cc3-ed5f-7689-ba44-0684a683e44d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Liabilities"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesAndStockholdersEquity_019e2cc3-ed5f-78e9-b25b-12fdf2334a3e" xlink:to="loc_us-gaap_Liabilities_019e2cc3-ed5f-7689-ba44-0684a683e44d" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CommitmentsAndContingencies_019e2cc3-ed5f-7c46-b85f-6ea079e33cca" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CommitmentsAndContingencies"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesAndStockholdersEquity_019e2cc3-ed5f-78e9-b25b-12fdf2334a3e" xlink:to="loc_us-gaap_CommitmentsAndContingencies_019e2cc3-ed5f-7c46-b85f-6ea079e33cca" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-776c-9bc8-b60cdd406d34" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_StockholdersEquity"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesAndStockholdersEquity_019e2cc3-ed5f-78e9-b25b-12fdf2334a3e" xlink:to="loc_us-gaap_StockholdersEquity_019e2cc3-ed5f-776c-9bc8-b60cdd406d34" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AssetsCurrent_019e2cc3-ed5f-7d48-91e1-481fa13caeb5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsCurrent"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_019e2cc3-ed5f-724b-9474-650c2a686cd6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsCurrent_019e2cc3-ed5f-7d48-91e1-481fa13caeb5" xlink:to="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_019e2cc3-ed5f-724b-9474-650c2a686cd6" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShortTermInvestments_019e2cc3-ed5f-7515-9281-b886aa604820" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShortTermInvestments"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsCurrent_019e2cc3-ed5f-7d48-91e1-481fa13caeb5" xlink:to="loc_us-gaap_ShortTermInvestments_019e2cc3-ed5f-7515-9281-b886aa604820" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PrepaidExpenseAndOtherAssetsCurrent_019e2cc3-ed5f-70da-abc3-e47c0451dd74" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsCurrent_019e2cc3-ed5f-7d48-91e1-481fa13caeb5" xlink:to="loc_us-gaap_PrepaidExpenseAndOtherAssetsCurrent_019e2cc3-ed5f-70da-abc3-e47c0451dd74" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-776d-8da5-8bd6c5055db4" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AssetsNoncurrent"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PropertyPlantAndEquipmentNet_019e2cc3-ed5f-78f0-9965-6e0a6d66bb65" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-776d-8da5-8bd6c5055db4" xlink:to="loc_us-gaap_PropertyPlantAndEquipmentNet_019e2cc3-ed5f-78f0-9965-6e0a6d66bb65" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLeaseRightOfUseAsset_019e2cc3-ed5f-7c79-a312-5638ab1c612b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseRightOfUseAsset"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-776d-8da5-8bd6c5055db4" xlink:to="loc_us-gaap_OperatingLeaseRightOfUseAsset_019e2cc3-ed5f-7c79-a312-5638ab1c612b" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LongTermInvestments_019e2cc3-ed5f-7d5e-b54a-e437722cc3fd" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LongTermInvestments"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-776d-8da5-8bd6c5055db4" xlink:to="loc_us-gaap_LongTermInvestments_019e2cc3-ed5f-7d5e-b54a-e437722cc3fd" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCashNoncurrent_019e2cc3-ed5f-7035-aa30-419dec5338d8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RestrictedCashNoncurrent"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-776d-8da5-8bd6c5055db4" xlink:to="loc_us-gaap_RestrictedCashNoncurrent_019e2cc3-ed5f-7035-aa30-419dec5338d8" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherAssetsNoncurrent_019e2cc3-ed5f-7ba6-8f07-13bd8c36d38b" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherAssetsNoncurrent"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AssetsNoncurrent_019e2cc3-ed5f-776d-8da5-8bd6c5055db4" xlink:to="loc_us-gaap_OtherAssetsNoncurrent_019e2cc3-ed5f-7ba6-8f07-13bd8c36d38b" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_Liabilities_019e2cc3-ed5f-7b56-84ef-3cda26e37701" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_Liabilities"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7502-a11f-5820bc3aaf63" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesCurrent"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_Liabilities_019e2cc3-ed5f-7b56-84ef-3cda26e37701" xlink:to="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7502-a11f-5820bc3aaf63" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLeaseLiabilityNoncurrent_019e2cc3-ed5f-7bf0-beef-2c144caab6fa" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_Liabilities_019e2cc3-ed5f-7b56-84ef-3cda26e37701" xlink:to="loc_us-gaap_OperatingLeaseLiabilityNoncurrent_019e2cc3-ed5f-7bf0-beef-2c144caab6fa" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7648-be97-2b5226186b9e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LiabilitiesCurrent"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccountsPayableCurrent_019e2cc3-ed5f-7da6-a63d-1889ffcc2dc0" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccountsPayableCurrent"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7648-be97-2b5226186b9e" xlink:to="loc_us-gaap_AccountsPayableCurrent_019e2cc3-ed5f-7da6-a63d-1889ffcc2dc0" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EmployeeRelatedLiabilitiesCurrent_019e2cc3-ed5f-72a7-96bd-4552e2f73dac" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EmployeeRelatedLiabilitiesCurrent"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7648-be97-2b5226186b9e" xlink:to="loc_us-gaap_EmployeeRelatedLiabilitiesCurrent_019e2cc3-ed5f-72a7-96bd-4552e2f73dac" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_AccruedContractManufacturingExpenses_019e2cc3-ed5f-7f8d-9676-097076ecaf7d" xlink:href="pcvx-20260630.xsd#pcvx_AccruedContractManufacturingExpenses"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7648-be97-2b5226186b9e" xlink:to="loc_pcvx_AccruedContractManufacturingExpenses_019e2cc3-ed5f-7f8d-9676-097076ecaf7d" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccruedLiabilitiesCurrent_019e2cc3-ed5f-7665-9238-905d0c4bd3d6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccruedLiabilitiesCurrent"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7648-be97-2b5226186b9e" xlink:to="loc_us-gaap_AccruedLiabilitiesCurrent_019e2cc3-ed5f-7665-9238-905d0c4bd3d6" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLeaseLiabilityCurrent_019e2cc3-ed5f-7b10-9b20-8c08cb8b9f9e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLiabilityCurrent"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LiabilitiesCurrent_019e2cc3-ed5f-7648-be97-2b5226186b9e" xlink:to="loc_us-gaap_OperatingLeaseLiabilityCurrent_019e2cc3-ed5f-7b10-9b20-8c08cb8b9f9e" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/CondensedConsolidatedStatementsofOperations" xlink:type="simple" xlink:href="pcvx-20260630.xsd#CondensedConsolidatedStatementsofOperations"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/CondensedConsolidatedStatementsofOperations" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingExpenses_019e2cc3-ed5f-7d2f-bfc7-8f0f05bc4ad6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingExpenses"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_GeneralAndAdministrativeExpense_019e2cc3-ed5f-704f-be1c-64986e8f4f8f" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GeneralAndAdministrativeExpense"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OperatingExpenses_019e2cc3-ed5f-7d2f-bfc7-8f0f05bc4ad6" xlink:to="loc_us-gaap_GeneralAndAdministrativeExpense_019e2cc3-ed5f-704f-be1c-64986e8f4f8f" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ResearchAndDevelopmentExpense_019e2cc3-ed5f-7fb4-8011-64628f96112e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ResearchAndDevelopmentExpense"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OperatingExpenses_019e2cc3-ed5f-7d2f-bfc7-8f0f05bc4ad6" xlink:to="loc_us-gaap_ResearchAndDevelopmentExpense_019e2cc3-ed5f-7fb4-8011-64628f96112e" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingIncomeLoss_019e2cc3-ed5f-72cb-a05a-cb50ebcb24df" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingExpenses_019e2cc3-ed5f-75e1-ad6f-852ccd99c1c3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingExpenses"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OperatingIncomeLoss_019e2cc3-ed5f-72cb-a05a-cb50ebcb24df" xlink:to="loc_us-gaap_OperatingExpenses_019e2cc3-ed5f-75e1-ad6f-852ccd99c1c3" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetIncomeLoss_019e2cc3-ed5f-7e0a-b341-0a4a56f8b010" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NonoperatingIncomeExpense_019e2cc3-ed5f-7b97-8534-0ca8a1c58bf7" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NonoperatingIncomeExpense"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetIncomeLoss_019e2cc3-ed5f-7e0a-b341-0a4a56f8b010" xlink:to="loc_us-gaap_NonoperatingIncomeExpense_019e2cc3-ed5f-7b97-8534-0ca8a1c58bf7" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingIncomeLoss_019e2cc3-ed5f-7554-b794-1c41d99b84d9" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingIncomeLoss"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetIncomeLoss_019e2cc3-ed5f-7e0a-b341-0a4a56f8b010" xlink:to="loc_us-gaap_OperatingIncomeLoss_019e2cc3-ed5f-7554-b794-1c41d99b84d9" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NonoperatingIncomeExpense_019e2cc3-ed5f-72d1-8f67-d199a03707e1" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NonoperatingIncomeExpense"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_InvestmentIncomeInterest_019e2cc3-ed5f-7d46-ba19-e3b468756ecd" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_InvestmentIncomeInterest"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NonoperatingIncomeExpense_019e2cc3-ed5f-72d1-8f67-d199a03707e1" xlink:to="loc_us-gaap_InvestmentIncomeInterest_019e2cc3-ed5f-7d46-ba19-e3b468756ecd" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherNonoperatingIncomeExpense_019e2cc3-ed5f-7188-bafc-d31b08b5c1fa" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherNonoperatingIncomeExpense"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NonoperatingIncomeExpense_019e2cc3-ed5f-72d1-8f67-d199a03707e1" xlink:to="loc_us-gaap_OtherNonoperatingIncomeExpense_019e2cc3-ed5f-7188-bafc-d31b08b5c1fa" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/CondensedConsolidatedStatementsofComprehensiveLoss" xlink:type="simple" xlink:href="pcvx-20260630.xsd#CondensedConsolidatedStatementsofComprehensiveLoss"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/CondensedConsolidatedStatementsofComprehensiveLoss" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ComprehensiveIncomeNetOfTax_019e2cc3-ed5f-789f-b2e5-86de5787516a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ComprehensiveIncomeNetOfTax"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetIncomeLoss_019e2cc3-ed5f-7535-b3d8-e9ee5e843793" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetIncomeLoss"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_ComprehensiveIncomeNetOfTax_019e2cc3-ed5f-789f-b2e5-86de5787516a" xlink:to="loc_us-gaap_NetIncomeLoss_019e2cc3-ed5f-7535-b3d8-e9ee5e843793" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodBeforeTax_019e2cc3-ed5f-74bf-bc5b-6fbe5da9a303" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodBeforeTax"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_ComprehensiveIncomeNetOfTax_019e2cc3-ed5f-789f-b2e5-86de5787516a" xlink:to="loc_us-gaap_OtherComprehensiveIncomeUnrealizedHoldingGainLossOnSecuritiesArisingDuringPeriodBeforeTax_019e2cc3-ed5f-74bf-bc5b-6fbe5da9a303" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax_019e2cc3-ed5f-74e9-9f7e-3b0e3a528e38" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_ComprehensiveIncomeNetOfTax_019e2cc3-ed5f-789f-b2e5-86de5787516a" xlink:to="loc_us-gaap_OtherComprehensiveIncomeLossForeignCurrencyTransactionAndTranslationAdjustmentNetOfTax_019e2cc3-ed5f-74e9-9f7e-3b0e3a528e38" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/CondensedConsolidatedStatementsofCashFlows" xlink:type="simple" xlink:href="pcvx-20260630.xsd#CondensedConsolidatedStatementsofCashFlows"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/CondensedConsolidatedStatementsofCashFlows" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents_019e2cc3-ed5f-7b0f-b88e-2ffb02ea8707" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_RestrictedCash_019e2cc3-ed5f-7698-a0ff-dbbf3e4f3dad" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_RestrictedCash"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents_019e2cc3-ed5f-7b0f-b88e-2ffb02ea8707" xlink:to="loc_us-gaap_RestrictedCash_019e2cc3-ed5f-7698-a0ff-dbbf3e4f3dad" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_019e2cc3-ed5f-714f-88e3-d1ea1800ee55" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents_019e2cc3-ed5f-7b0f-b88e-2ffb02ea8707" xlink:to="loc_us-gaap_CashAndCashEquivalentsAtCarryingValue_019e2cc3-ed5f-714f-88e3-d1ea1800ee55" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ForeignCurrencyTransactionGainLossUnrealizedAfterTax_019e2cc3-ed5f-7751-8a62-201819a4612a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ForeignCurrencyTransactionGainLossUnrealizedAfterTax"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_ForeignCurrencyTransactionGainLossUnrealizedAfterTax_019e2cc3-ed5f-7751-8a62-201819a4612a" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ShareBasedCompensation_019e2cc3-ed5f-7333-8d29-2385b35b83eb" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ShareBasedCompensation"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_ShareBasedCompensation_019e2cc3-ed5f-7333-8d29-2385b35b83eb" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProfitLoss_019e2cc3-ed5f-7d06-bce0-081f9020bf06" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProfitLoss"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_ProfitLoss_019e2cc3-ed5f-7d06-bce0-081f9020bf06" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments_019e2cc3-ed5f-7acb-b56b-1765acd49db6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments"/>
    <link:calculationArc order="4" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_AccretionAmortizationOfDiscountsAndPremiumsInvestments_019e2cc3-ed5f-7acb-b56b-1765acd49db6" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInAccruedLiabilities_019e2cc3-ed5f-71ac-b41e-47b7154733ce" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilities"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_IncreaseDecreaseInAccruedLiabilities_019e2cc3-ed5f-71ac-b41e-47b7154733ce" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_DepreciationDepletionAndAmortization_019e2cc3-ed5f-7044-847c-05eeabf001a8" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_DepreciationDepletionAndAmortization"/>
    <link:calculationArc order="6" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_DepreciationDepletionAndAmortization_019e2cc3-ed5f-7044-847c-05eeabf001a8" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_IncreaseDecreaseInOperatingLeaseRightOfUseAsset_019e2cc3-ed5f-7e59-9b26-26a4c4f59e9b" xlink:href="pcvx-20260630.xsd#pcvx_IncreaseDecreaseInOperatingLeaseRightOfUseAsset"/>
    <link:calculationArc order="7" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_pcvx_IncreaseDecreaseInOperatingLeaseRightOfUseAsset_019e2cc3-ed5f-7e59-9b26-26a4c4f59e9b" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense_019e2cc3-ed5f-757f-a1bd-38e2474729a3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense"/>
    <link:calculationArc order="8" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_OperatingLeaseRightOfUseAssetAmortizationExpense_019e2cc3-ed5f-757f-a1bd-38e2474729a3" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInOtherOperatingAssets_019e2cc3-ed5f-7677-bd76-d9d50d10f833" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInOtherOperatingAssets"/>
    <link:calculationArc order="9" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_IncreaseDecreaseInOtherOperatingAssets_019e2cc3-ed5f-7677-bd76-d9d50d10f833" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets_019e2cc3-ed5f-755f-9d18-eb7e1d1ee77c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets"/>
    <link:calculationArc order="10" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets_019e2cc3-ed5f-755f-9d18-eb7e1d1ee77c" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInAccountsPayable_019e2cc3-ed5f-7cd4-9b36-15b074fbe2c9" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInAccountsPayable"/>
    <link:calculationArc order="11" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_IncreaseDecreaseInAccountsPayable_019e2cc3-ed5f-7cd4-9b36-15b074fbe2c9" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_IncreaseDecreaseInAccruedCompensation_019e2cc3-ed5f-7c0f-94f5-f62bcbce5c11" xlink:href="pcvx-20260630.xsd#pcvx_IncreaseDecreaseInAccruedCompensation"/>
    <link:calculationArc order="12" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_pcvx_IncreaseDecreaseInAccruedCompensation_019e2cc3-ed5f-7c0f-94f5-f62bcbce5c11" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_IncreaseDecreaseInOperatingLeaseLiability_019e2cc3-ed5f-704d-ad0c-c46524a552fe" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_IncreaseDecreaseInOperatingLeaseLiability"/>
    <link:calculationArc order="13" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_us-gaap_IncreaseDecreaseInOperatingLeaseLiability_019e2cc3-ed5f-704d-ad0c-c46524a552fe" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_IncreaseDecreaseInAccruedContractManufacturingExpenses_019e2cc3-ed5f-7813-90df-cb6f09f25b36" xlink:href="pcvx-20260630.xsd#pcvx_IncreaseDecreaseInAccruedContractManufacturingExpenses"/>
    <link:calculationArc order="14" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-7c51-be47-a12759e985ad" xlink:to="loc_pcvx_IncreaseDecreaseInAccruedContractManufacturingExpenses_019e2cc3-ed5f-7813-90df-cb6f09f25b36" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-72ee-805e-dbfea1867d81" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt_019e2cc3-ed5f-73f6-a899-31eeda5a24df" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-72ee-805e-dbfea1867d81" xlink:to="loc_us-gaap_PaymentsToAcquireAvailableForSaleSecuritiesDebt_019e2cc3-ed5f-73f6-a899-31eeda5a24df" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProceedsFromSaleOfAvailableForSaleSecuritiesDebt_019e2cc3-ed5f-72e6-801c-4905ba39241d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromSaleOfAvailableForSaleSecuritiesDebt"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-72ee-805e-dbfea1867d81" xlink:to="loc_us-gaap_ProceedsFromSaleOfAvailableForSaleSecuritiesDebt_019e2cc3-ed5f-72e6-801c-4905ba39241d" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities_019e2cc3-ed5f-7ab5-b27e-3e331df21181" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-72ee-805e-dbfea1867d81" xlink:to="loc_us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities_019e2cc3-ed5f-7ab5-b27e-3e331df21181" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_PaymentsToAcquireManufacturingFacilityAndEquipment_019e2cc3-ed5f-7f8f-abf9-d3bf7f6ae0a6" xlink:href="pcvx-20260630.xsd#pcvx_PaymentsToAcquireManufacturingFacilityAndEquipment"/>
    <link:calculationArc order="4" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-72ee-805e-dbfea1867d81" xlink:to="loc_pcvx_PaymentsToAcquireManufacturingFacilityAndEquipment_019e2cc3-ed5f-7f8f-abf9-d3bf7f6ae0a6" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsToAcquirePropertyPlantAndEquipment_019e2cc3-ed5f-71ad-ae21-c42c68f9c876" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment"/>
    <link:calculationArc order="5" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-72ee-805e-dbfea1867d81" xlink:to="loc_us-gaap_PaymentsToAcquirePropertyPlantAndEquipment_019e2cc3-ed5f-71ad-ae21-c42c68f9c876" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetCashProvidedByUsedInFinancingActivities_019e2cc3-ed5f-7171-8b57-b82b85e8efd5" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation_019e2cc3-ed5f-7b86-9d1d-9817096c5cda" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInFinancingActivities_019e2cc3-ed5f-7171-8b57-b82b85e8efd5" xlink:to="loc_us-gaap_PaymentsRelatedToTaxWithholdingForShareBasedCompensation_019e2cc3-ed5f-7b86-9d1d-9817096c5cda" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_ProceedsFromStockPlans_019e2cc3-ed5f-727a-8a3b-11ec7841257f" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_ProceedsFromStockPlans"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInFinancingActivities_019e2cc3-ed5f-7171-8b57-b82b85e8efd5" xlink:to="loc_us-gaap_ProceedsFromStockPlans_019e2cc3-ed5f-727a-8a3b-11ec7841257f" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_ProceedsFromIssuanceOfCommonStockFromFollowOnOfferingNetOfIssuanceCosts_019e2cc3-ed5f-7792-9d22-3912ebad488a" xlink:href="pcvx-20260630.xsd#pcvx_ProceedsFromIssuanceOfCommonStockFromFollowOnOfferingNetOfIssuanceCosts"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_NetCashProvidedByUsedInFinancingActivities_019e2cc3-ed5f-7171-8b57-b82b85e8efd5" xlink:to="loc_pcvx_ProceedsFromIssuanceOfCommonStockFromFollowOnOfferingNetOfIssuanceCosts_019e2cc3-ed5f-7792-9d22-3912ebad488a" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect_019e2cc3-ed5f-7df4-892e-7b37eca0ddb3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-71d8-9a63-253bf7fc12be" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect_019e2cc3-ed5f-7df4-892e-7b37eca0ddb3" xlink:to="loc_us-gaap_NetCashProvidedByUsedInOperatingActivities_019e2cc3-ed5f-71d8-9a63-253bf7fc12be" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-7be3-a0ec-b4c65ed2d985" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect_019e2cc3-ed5f-7df4-892e-7b37eca0ddb3" xlink:to="loc_us-gaap_NetCashProvidedByUsedInInvestingActivities_019e2cc3-ed5f-7be3-a0ec-b4c65ed2d985" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_NetCashProvidedByUsedInFinancingActivities_019e2cc3-ed5f-7fbc-8e75-6c4e542747ad" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect_019e2cc3-ed5f-7df4-892e-7b37eca0ddb3" xlink:to="loc_us-gaap_NetCashProvidedByUsedInFinancingActivities_019e2cc3-ed5f-7fbc-8e75-6c4e542747ad" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents_019e2cc3-ed5f-7f13-8742-9543fefd5336" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseIncludingExchangeRateEffect_019e2cc3-ed5f-7df4-892e-7b37eca0ddb3" xlink:to="loc_us-gaap_EffectOfExchangeRateOnCashCashEquivalentsRestrictedCashAndRestrictedCashEquivalents_019e2cc3-ed5f-7f13-8742-9543fefd5336" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofFinancialInstrumentsMeasuredatFairValueonRecurringBasisDetails" xlink:type="simple" xlink:href="pcvx-20260630.xsd#FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofFinancialInstrumentsMeasuredatFairValueonRecurringBasisDetails"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofFinancialInstrumentsMeasuredatFairValueonRecurringBasisDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-7f56-a6eb-23c699edd969" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-75bd-8371-e5d1baf4c104" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-7f56-a6eb-23c699edd969" xlink:to="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-75bd-8371-e5d1baf4c104" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-721c-aa17-29f3d808abb6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-7f56-a6eb-23c699edd969" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-721c-aa17-29f3d808abb6" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis_019e2cc3-ed5f-780e-95b5-fe8a0183ee87" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-76e1-8ebe-2d6f6c163414" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis_019e2cc3-ed5f-780e-95b5-fe8a0183ee87" xlink:to="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-76e1-8ebe-2d6f6c163414" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-7362-ac6d-f9767a4a2c0b" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis_019e2cc3-ed5f-780e-95b5-fe8a0183ee87" xlink:to="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-7362-ac6d-f9767a4a2c0b" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestments_019e2cc3-ed5f-7de2-82eb-c839ba622483" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestments"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis_019e2cc3-ed5f-780e-95b5-fe8a0183ee87" xlink:to="loc_pcvx_CashAndCashEquivalentsAndInvestments_019e2cc3-ed5f-7de2-82eb-c839ba622483" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-73b2-bea5-7e2bb3b1a3af" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-79c1-928e-05180b5c4ab7" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-73b2-bea5-7e2bb3b1a3af" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-79c1-928e-05180b5c4ab7" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-7ee6-8d60-5ea86a1780da" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-73b2-bea5-7e2bb3b1a3af" xlink:to="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-7ee6-8d60-5ea86a1780da" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestments_019e2cc3-ed5f-79df-b6e1-a5cc843299a9" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestments"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_019e2cc3-ed5f-7f5e-a405-660bddb3de2f" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestments_019e2cc3-ed5f-79df-b6e1-a5cc843299a9" xlink:to="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_019e2cc3-ed5f-7f5e-a405-660bddb3de2f" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e2cc3-ed5f-7218-99bf-45af84ef8282" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestments_019e2cc3-ed5f-79df-b6e1-a5cc843299a9" xlink:to="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e2cc3-ed5f-7218-99bf-45af84ef8282" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAmortizedCost_019e2cc3-ed5f-70e1-b539-6a529e9d1436" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAmortizedCost"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-704c-84ad-bac01c080b53" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAmortizedCost_019e2cc3-ed5f-70e1-b539-6a529e9d1436" xlink:to="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-704c-84ad-bac01c080b53" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-7f53-a6f8-7d92089ac2d7" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAmortizedCost_019e2cc3-ed5f-70e1-b539-6a529e9d1436" xlink:to="loc_pcvx_CashAndCashEquivalentsGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-7f53-a6f8-7d92089ac2d7" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_019e2cc3-ed5f-78b9-a8d3-1a885969036d" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAmortizedCost_019e2cc3-ed5f-70e1-b539-6a529e9d1436" xlink:to="loc_us-gaap_CashAndCashEquivalentsFairValueDisclosure_019e2cc3-ed5f-78b9-a8d3-1a885969036d" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e2cc3-ed5f-70c3-a525-41c39c5b63e6" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-762f-8b05-374065eb4534" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <link:calculationArc order="1" weight="-1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e2cc3-ed5f-70c3-a525-41c39c5b63e6" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax_019e2cc3-ed5f-762f-8b05-374065eb4534" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-789e-9ab7-cd7d61797b03" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e2cc3-ed5f-70c3-a525-41c39c5b63e6" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax_019e2cc3-ed5f-789e-9ab7-cd7d61797b03" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e2cc3-ed5f-752a-a4d0-4d5d4722c83e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e2cc3-ed5f-70c3-a525-41c39c5b63e6" xlink:to="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e2cc3-ed5f-752a-a4d0-4d5d4722c83e" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofFinancialInstrumentsMeasuredatFairValueonRecurringBasisDetails_1" xlink:type="simple" xlink:href="pcvx-20260630.xsd#FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofFinancialInstrumentsMeasuredatFairValueonRecurringBasisDetails_1"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofFinancialInstrumentsMeasuredatFairValueonRecurringBasisDetails_1" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis_019e2cc3-ed5f-73da-8142-64d18aad5ff2" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e2cc3-ed5f-74a2-8104-e66440f0febe" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis_019e2cc3-ed5f-73da-8142-64d18aad5ff2" xlink:to="loc_us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis_019e2cc3-ed5f-74a2-8104-e66440f0febe" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_CashAndCashEquivalentsAmortizedCost_019e2cc3-ed5f-72d9-a07c-8b6e8c81d809" xlink:href="pcvx-20260630.xsd#pcvx_CashAndCashEquivalentsAmortizedCost"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_pcvx_CashAndCashEquivalentsAndInvestmentsAmortizedCostBasis_019e2cc3-ed5f-73da-8142-64d18aad5ff2" xlink:to="loc_pcvx_CashAndCashEquivalentsAmortizedCost_019e2cc3-ed5f-72d9-a07c-8b6e8c81d809" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofContractualMaturitiesofInvestmentsDetails" xlink:type="simple" xlink:href="pcvx-20260630.xsd#FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofContractualMaturitiesofInvestmentsDetails"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/FairValueMeasurementsandFairValueofFinancialInstrumentsScheduleofContractualMaturitiesofInvestmentsDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e2cc3-ed5f-7e6b-9202-4529af291b4c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearFairValue_019e2cc3-ed5f-7381-a09d-4d50b4c64f95" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearFairValue"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e2cc3-ed5f-7e6b-9202-4529af291b4c" xlink:to="loc_us-gaap_AvailableForSaleSecuritiesDebtMaturitiesWithinOneYearFairValue_019e2cc3-ed5f-7381-a09d-4d50b4c64f95" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughFiveYearsFairValue_019e2cc3-ed5f-76d1-bdef-5f0a3acc70da" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughFiveYearsFairValue"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_AvailableForSaleSecuritiesDebtSecurities_019e2cc3-ed5f-7e6b-9202-4529af291b4c" xlink:to="loc_us-gaap_AvailableForSaleSecuritiesDebtMaturitiesAfterOneThroughFiveYearsFairValue_019e2cc3-ed5f-76d1-bdef-5f0a3acc70da" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/LeasesScheduleofMaturitiesofLeaseLiabilitiesDetails" xlink:type="simple" xlink:href="pcvx-20260630.xsd#LeasesScheduleofMaturitiesofLeaseLiabilitiesDetails"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/LeasesScheduleofMaturitiesofLeaseLiabilitiesDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7153-b843-7db10b431efe" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount_019e2cc3-ee19-740c-b41c-69ba8d494130" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7153-b843-7db10b431efe" xlink:to="loc_us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount_019e2cc3-ee19-740c-b41c-69ba8d494130" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingLeaseLiability_019e2cc3-ee19-7b16-88da-dfd839f2f91a" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingLeaseLiability"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7153-b843-7db10b431efe" xlink:to="loc_us-gaap_OperatingLeaseLiability_019e2cc3-ee19-7b16-88da-dfd839f2f91a" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/LeasesScheduleofMaturitiesofLeaseLiabilitiesDetails_1" xlink:type="simple" xlink:href="pcvx-20260630.xsd#LeasesScheduleofMaturitiesofLeaseLiabilitiesDetails_1"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/LeasesScheduleofMaturitiesofLeaseLiabilitiesDetails_1" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7610-a94f-29d4885ae7b3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour_019e2cc3-ee19-79f0-9958-ced40fb58d97" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7610-a94f-29d4885ae7b3" xlink:to="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour_019e2cc3-ee19-79f0-9958-ced40fb58d97" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree_019e2cc3-ee19-7704-adb7-d6eda7b46af2" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7610-a94f-29d4885ae7b3" xlink:to="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree_019e2cc3-ee19-7704-adb7-d6eda7b46af2" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo_019e2cc3-ee19-799c-976d-0293e42ed7b7" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7610-a94f-29d4885ae7b3" xlink:to="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo_019e2cc3-ee19-799c-976d-0293e42ed7b7" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths_019e2cc3-ee19-7e4f-bfc0-c84b8da1d178" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7610-a94f-29d4885ae7b3" xlink:to="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths_019e2cc3-ee19-7e4f-bfc0-c84b8da1d178" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear_019e2cc3-ee19-790d-98f9-b397ef9e5a39" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7610-a94f-29d4885ae7b3" xlink:to="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear_019e2cc3-ee19-790d-98f9-b397ef9e5a39" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_LesseeOperatingLeaseLiabilityToBePaidAfterYearFour_019e2cc3-ee19-7872-b157-6ad6202969cd" xlink:href="pcvx-20260630.xsd#pcvx_LesseeOperatingLeaseLiabilityToBePaidAfterYearFour"/>
    <link:calculationArc order="6" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue_019e2cc3-ee19-7610-a94f-29d4885ae7b3" xlink:to="loc_pcvx_LesseeOperatingLeaseLiabilityToBePaidAfterYearFour_019e2cc3-ee19-7872-b157-6ad6202969cd" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/CommitmentsandContingenciesScheduleofLongTermPurchaseCommitmentDetails" xlink:type="simple" xlink:href="pcvx-20260630.xsd#CommitmentsandContingenciesScheduleofLongTermPurchaseCommitmentDetails"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/CommitmentsandContingenciesScheduleofLongTermPurchaseCommitmentDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitment_019e2cc3-ee19-7c95-9ff8-65e4a2942765" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherCommitment"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentsFutureMinimumPaymentsRemainderOfFiscalYear_019e2cc3-ee19-7984-b7b9-f993a951bb6c" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherCommitmentsFutureMinimumPaymentsRemainderOfFiscalYear"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OtherCommitment_019e2cc3-ee19-7c95-9ff8-65e4a2942765" xlink:to="loc_us-gaap_OtherCommitmentsFutureMinimumPaymentsRemainderOfFiscalYear_019e2cc3-ee19-7984-b7b9-f993a951bb6c" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentDueInNextTwelveMonths_019e2cc3-ee19-7899-a911-e314efc1fe50" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherCommitmentDueInNextTwelveMonths"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OtherCommitment_019e2cc3-ee19-7c95-9ff8-65e4a2942765" xlink:to="loc_us-gaap_OtherCommitmentDueInNextTwelveMonths_019e2cc3-ee19-7899-a911-e314efc1fe50" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentDueInSecondYear_019e2cc3-ee19-7ffd-9490-bd2b1ce7a87e" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherCommitmentDueInSecondYear"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OtherCommitment_019e2cc3-ee19-7c95-9ff8-65e4a2942765" xlink:to="loc_us-gaap_OtherCommitmentDueInSecondYear_019e2cc3-ee19-7ffd-9490-bd2b1ce7a87e" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OtherCommitmentDueInThirdYear_019e2cc3-ee19-7f95-bfc5-7ecf614bc4a7" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OtherCommitmentDueInThirdYear"/>
    <link:calculationArc order="4" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OtherCommitment_019e2cc3-ee19-7c95-9ff8-65e4a2942765" xlink:to="loc_us-gaap_OtherCommitmentDueInThirdYear_019e2cc3-ee19-7f95-bfc5-7ecf614bc4a7" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_OtherCommitmentToBePaidAfterYearThree_019e2cc3-ee19-7f47-b535-cf78999e0748" xlink:href="pcvx-20260630.xsd#pcvx_OtherCommitmentToBePaidAfterYearThree"/>
    <link:calculationArc order="5" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OtherCommitment_019e2cc3-ee19-7c95-9ff8-65e4a2942765" xlink:to="loc_pcvx_OtherCommitmentToBePaidAfterYearThree_019e2cc3-ee19-7f47-b535-cf78999e0748" xlink:type="arc"/>
  </link:calculationLink>
  <link:roleRef roleURI="http://www.vaxcyte.com/role/SegmentReportingScheduleofDisaggregationofIncomeStatementExpensesDetails" xlink:type="simple" xlink:href="pcvx-20260630.xsd#SegmentReportingScheduleofDisaggregationofIncomeStatementExpensesDetails"/>
  <link:calculationLink xlink:role="http://www.vaxcyte.com/role/SegmentReportingScheduleofDisaggregationofIncomeStatementExpensesDetails" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_OperatingExpenses_019fc8da-0756-75a1-be2f-b6e723b24178" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_OperatingExpenses"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_ExternalResearchAndDevelopmentExpense_019fc8da-0756-71a4-b723-e922ad0a3927" xlink:href="pcvx-20260630.xsd#pcvx_ExternalResearchAndDevelopmentExpense"/>
    <link:calculationArc order="1" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OperatingExpenses_019fc8da-0756-75a1-be2f-b6e723b24178" xlink:to="loc_pcvx_ExternalResearchAndDevelopmentExpense_019fc8da-0756-71a4-b723-e922ad0a3927" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_pcvx_InternalResearchAndDevelopmentExpense_019fc8da-0756-7ec6-b97f-a4efff222eb7" xlink:href="pcvx-20260630.xsd#pcvx_InternalResearchAndDevelopmentExpense"/>
    <link:calculationArc order="2" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OperatingExpenses_019fc8da-0756-75a1-be2f-b6e723b24178" xlink:to="loc_pcvx_InternalResearchAndDevelopmentExpense_019fc8da-0756-7ec6-b97f-a4efff222eb7" xlink:type="arc"/>
    <link:loc xlink:type="locator" xlink:label="loc_us-gaap_GeneralAndAdministrativeExpense_019fc8da-0756-7313-b3b0-2a3849eb44e3" xlink:href="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd#us-gaap_GeneralAndAdministrativeExpense"/>
    <link:calculationArc order="3" weight="1.0" xlink:arcrole="https://xbrl.org/2023/arcrole/summation-item" xlink:from="loc_us-gaap_OperatingExpenses_019fc8da-0756-75a1-be2f-b6e723b24178" xlink:to="loc_us-gaap_GeneralAndAdministrativeExpense_019fc8da-0756-7313-b3b0-2a3849eb44e3" xlink:type="arc"/>
  </link:calculationLink>
</link:linkbase>
