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

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2026 Workiva-->
<!--r:019e8471-58ff-7291-a785-8fac5b1ca99b,g:1b3c011e-74c9-4fc8-9b01-8fa32d0aed90-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:jkhy="http://www.jackhenry.com/20260626" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2024-01-31" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://www.jackhenry.com/20260626">
  <xs:import namespace="http://fasb.org/srt/2026" schemaLocation="https://xbrl.fasb.org/srt/2026/elts/srt-2026.xsd"/>
  <xs:import namespace="http://fasb.org/us-gaap-ebp/2026" schemaLocation="https://xbrl.fasb.org/us-gaap/2026/ebp/elts/us-gaap-ebp-2026.xsd"/>
  <xs:import namespace="http://fasb.org/us-gaap/2026" schemaLocation="https://xbrl.fasb.org/us-gaap/2026/elts/us-gaap-2026.xsd"/>
  <xs:import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/2003/linkbase" schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/dtr/type/2024-01-31" schemaLocation="https://www.xbrl.org/dtr/type/2024-01-31/types.xsd"/>
  <xs:import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd"/>
  <xs:import namespace="http://xbrl.sec.gov/dei/2026" schemaLocation="https://xbrl.sec.gov/dei/2026/dei-2026.xsd"/>
  <xs:annotation>
    <xs:appinfo>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20260626_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20260626_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20260626_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20260626_cal.xml" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:type="simple"/>
      <link:roleType id="COVER" roleURI="http://www.jackhenry.com/role/COVER">
        <link:definition>0000001 - Document - COVER</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="STATEMENTSOFNETASSETSAVAILABLEFORBENEFITS" roleURI="http://www.jackhenry.com/role/STATEMENTSOFNETASSETSAVAILABLEFORBENEFITS">
        <link:definition>0000002 - Statement - STATEMENTS OF NET ASSETS AVAILABLE FOR BENEFITS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="STATEMENTOFCHANGESINNETASSETSAVAILABLEFORBENEFITS" roleURI="http://www.jackhenry.com/role/STATEMENTOFCHANGESINNETASSETSAVAILABLEFORBENEFITS">
        <link:definition>0000003 - Statement - STATEMENT OF CHANGES IN NET ASSETS AVAILABLE FOR BENEFITS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="DESCRIPTIONOFPLAN" roleURI="http://www.jackhenry.com/role/DESCRIPTIONOFPLAN">
        <link:definition>0000004 - Disclosure - DESCRIPTION OF PLAN</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SIGNIFICANTACCOUNTINGPOLICIES" roleURI="http://www.jackhenry.com/role/SIGNIFICANTACCOUNTINGPOLICIES">
        <link:definition>0000005 - Disclosure - SIGNIFICANT ACCOUNTING POLICIES</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FAIRVALUEMEASUREMENTS" roleURI="http://www.jackhenry.com/role/FAIRVALUEMEASUREMENTS">
        <link:definition>0000006 - Disclosure - FAIR VALUE MEASUREMENTS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="STABLEVALUEFUNDINVESTMENTCONTRACTDISCLOSURE" roleURI="http://www.jackhenry.com/role/STABLEVALUEFUNDINVESTMENTCONTRACTDISCLOSURE">
        <link:definition>0000007 - Disclosure - STABLE VALUE FUND / INVESTMENT CONTRACT DISCLOSURE</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EXEMPTPARTIESININTERESTTRANSACTIONS" roleURI="http://www.jackhenry.com/role/EXEMPTPARTIESININTERESTTRANSACTIONS">
        <link:definition>0000008 - Disclosure - EXEMPT PARTIES-IN-INTEREST TRANSACTIONS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="PLANTERMINATION" roleURI="http://www.jackhenry.com/role/PLANTERMINATION">
        <link:definition>0000009 - Disclosure - PLAN TERMINATION</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FEDERALINCOMETAXSTATUS" roleURI="http://www.jackhenry.com/role/FEDERALINCOMETAXSTATUS">
        <link:definition>0000010 - Disclosure - FEDERAL INCOME TAX STATUS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NETASSETVALUENAVPERSHARE" roleURI="http://www.jackhenry.com/role/NETASSETVALUENAVPERSHARE">
        <link:definition>0000011 - Disclosure - NET ASSET VALUE (NAV) PER SHARE</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CONCENTRATIONOFMARKETRISK" roleURI="http://www.jackhenry.com/role/CONCENTRATIONOFMARKETRISK">
        <link:definition>0000012 - Disclosure - CONCENTRATION OF MARKET RISK</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FORM5500SCHEDULEHPARTIVLINE4iSCHEDULEOFASSETSHELDATENDOFYEAR" roleURI="http://www.jackhenry.com/role/FORM5500SCHEDULEHPARTIVLINE4iSCHEDULEOFASSETSHELDATENDOFYEAR">
        <link:definition>0000013 - Disclosure - FORM 5500, SCHEDULE H, PART IV, LINE 4i - SCHEDULE OF ASSETS (HELD AT END OF YEAR)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SIGNIFICANTACCOUNTINGPOLICIESPolicies" roleURI="http://www.jackhenry.com/role/SIGNIFICANTACCOUNTINGPOLICIESPolicies">
        <link:definition>0000014 - Disclosure - SIGNIFICANT ACCOUNTING POLICIES (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FAIRVALUEMEASUREMENTSTables" roleURI="http://www.jackhenry.com/role/FAIRVALUEMEASUREMENTSTables">
        <link:definition>0000015 - Disclosure - FAIR VALUE MEASUREMENTS (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NETASSETVALUENAVPERSHARETables" roleURI="http://www.jackhenry.com/role/NETASSETVALUENAVPERSHARETables">
        <link:definition>0000016 - Disclosure - NET ASSET VALUE (NAV) PER SHARE (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="DESCRIPTIONOFPLANDetails" roleURI="http://www.jackhenry.com/role/DESCRIPTIONOFPLANDetails">
        <link:definition>0000017 - Disclosure - DESCRIPTION OF PLAN (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FAIRVALUEMEASUREMENTSDetails" roleURI="http://www.jackhenry.com/role/FAIRVALUEMEASUREMENTSDetails">
        <link:definition>0000018 - Disclosure - FAIR VALUE MEASUREMENTS (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="STABLEVALUEFUNDINVESTMENTCONTRACTDISCLOSUREDetails" roleURI="http://www.jackhenry.com/role/STABLEVALUEFUNDINVESTMENTCONTRACTDISCLOSUREDetails">
        <link:definition>0000019 - Disclosure - STABLE VALUE FUND / INVESTMENT CONTRACT DISCLOSURE (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EXEMPTPARTIESININTERESTTRANSACTIONSDetails" roleURI="http://www.jackhenry.com/role/EXEMPTPARTIESININTERESTTRANSACTIONSDetails">
        <link:definition>0000020 - Disclosure - EXEMPT PARTIES-IN-INTEREST TRANSACTIONS (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NETASSETVALUENAVPERSHAREDetails" roleURI="http://www.jackhenry.com/role/NETASSETVALUENAVPERSHAREDetails">
        <link:definition>0000021 - Disclosure - NET ASSET VALUE (NAV) PER SHARE (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CONCENTRATIONOFMARKETRISKDetails" roleURI="http://www.jackhenry.com/role/CONCENTRATIONOFMARKETRISKDetails">
        <link:definition>0000022 - Disclosure - CONCENTRATION OF MARKET RISK (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FORM5500SCHEDULEHPARTIVLINE4iSCHEDULEOFASSETSHELDATENDOFYEARDetails" roleURI="http://www.jackhenry.com/role/FORM5500SCHEDULEHPARTIVLINE4iSCHEDULEOFASSETSHELDATENDOFYEARDetails">
        <link:definition>0000023 - Disclosure - FORM 5500, SCHEDULE H, PART IV, LINE 4i - SCHEDULE OF ASSETS (HELD AT END OF YEAR) (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FORM5500SCHEDULEHPARTIVLINE4iSCHEDULEOFASSETSHELDATENDOFYEARDetails_1" roleURI="http://www.jackhenry.com/role/FORM5500SCHEDULEHPARTIVLINE4iSCHEDULEOFASSETSHELDATENDOFYEARDetails_1">
        <link:definition>0000023 - Disclosure - FORM 5500, SCHEDULE H, PART IV, LINE 4i - SCHEDULE OF ASSETS (HELD AT END OF YEAR) (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xs:appinfo>
  </xs:annotation>
  <xs:element id="jkhy_EBP003Member" abstract="true" name="EBP003Member" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_EBPEmployerContributionTypeAxis" abstract="true" name="EBPEmployerContributionTypeAxis" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrldt:dimensionItem" type="xbrli:stringItemType"/>
  <xs:element id="jkhy_EBPEmployerContributionTypeDomain" abstract="true" name="EBPEmployerContributionTypeDomain" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_EBPQualifiedNonElectiveContributionsMember" abstract="true" name="EBPQualifiedNonElectiveContributionsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_EBPEmployerMatchingContributionMember" abstract="true" name="EBPEmployerMatchingContributionMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_EBPEmployeeEligibility" abstract="false" name="EBPEmployeeEligibility" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_EBPRequisiteServicePeriod" abstract="false" name="EBPRequisiteServicePeriod" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_EBPRequisiteServiceHours" abstract="false" name="EBPRequisiteServiceHours" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:integerItemType"/>
  <xs:element id="jkhy_EBPDividendRecordDateVestingPercentage" abstract="false" name="EBPDividendRecordDateVestingPercentage" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="jkhy_EBPParticipantContributionAutomaticAnnualIncreaseDeferralRate" abstract="false" name="EBPParticipantContributionAutomaticAnnualIncreaseDeferralRate" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="jkhy_EBPParticipantContributionMaximumContributionToEligibleCompensationPercentage" abstract="false" name="EBPParticipantContributionMaximumContributionToEligibleCompensationPercentage" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="jkhy_EBPEmployerContributionVestingPercentage" abstract="false" name="EBPEmployerContributionVestingPercentage" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="jkhy_EBPEmployerContributionVestingServicePeriod" abstract="false" name="EBPEmployerContributionVestingServicePeriod" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_EBPNoteReceivableFromParticipantGeneralLoanMinimumBorrowingTerm" abstract="false" name="EBPNoteReceivableFromParticipantGeneralLoanMinimumBorrowingTerm" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_EBPNoteReceivableFromParticipantGeneralLoanMaximumBorrowingTerm" abstract="false" name="EBPNoteReceivableFromParticipantGeneralLoanMaximumBorrowingTerm" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_EBPNoteReceivableFromParticipantAccountPrimaryResidenceMaximumBorrowingTerm" abstract="false" name="EBPNoteReceivableFromParticipantAccountPrimaryResidenceMaximumBorrowingTerm" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_EBPCreditingInterestRate" abstract="false" name="EBPCreditingInterestRate" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:percentItemType"/>
  <xs:element id="jkhy_DomesticStockFundsMember" abstract="true" name="DomesticStockFundsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_MutualFundsPooledSeparateAccountAndCollectiveTrustFairValueMember" abstract="true" name="MutualFundsPooledSeparateAccountAndCollectiveTrustFairValueMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_StableValueFundFairValueMember" abstract="true" name="StableValueFundFairValueMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
</xs:schema>
