Exhibit 10.1

September 9, 2026

Thomas A. Fitzgerald

Re: Separation and Transition Services Agreement

Dear Tom:

This letter agreement follows our conversation of August 19, 2026, regarding your employment with TransCode Therapeutics, Inc. (the “Company”) and confirms the termination of your employment with the Company effective September 9, 2026 (the “Separation Date”). We appreciate your contributions and would like to work with you to make this transition as smooth as possible.

Regardless of whether you sign this Agreement (as defined below): (i) you and we are subject to continuing obligations under your Employment Agreement with the Company dated March 24, 2021 (the “Employment Agreement”) and your Employee Confidentiality and Intellectual Property Assignment Agreement with the Company (the “Confidentiality Agreement” and with any other confidentiality, restrictive covenant and other ongoing common law or fiduciary obligations you have to any of the Releasees (as defined below), the “Ongoing Obligations”); and (ii) your equity rights remain subject to the applicable equity agreement and the Company’s equity plan (the “Equity Documents”) in all respects, except in the case of this clause (ii) as may be expressly modified by this Agreement.

The Company shall, if it has not already done so, pay or provide you with the “Accrued Obligations” described in the Employment Agreement: (i) all accrued but unpaid salary as of the Separation Date, (ii) accrued but unused paid time off, and (iii) any equity rights vested prior to the Separation Date, subject to the Equity Documents and this Agreement.

The remainder of this letter proposes an agreement (the “Agreement”) between you and the Company. You and the Company agree as follows:

1.            Severance Benefits

(a)           Severance Pay.

The Company will pay you an aggregate severance payment (to which, absent your signing this Agreement, you would not otherwise be entitled) totaling $1,250,000 (the “Severance Pay”). The Severance Pay shall be subject to taxes and lawful withholdings; all amounts listed below are gross (before taxes). The Company shall pay the Severance Pay in installments as follows and subject to the following terms and conditions :

“$5 Million Financing” means the Company’s cumulative receipt of Qualified Funding of at least $5,000,000 following the Separation Date.

“$10 Million Financing” means the Company’s cumulative receipt of Qualified Funding of at least $10,000,000 following the Separation Date.

“Qualified Funding” means gross funding from any source(s), including but not limited to (i) the sale of securities, whether in a single transaction or a series of related transactions, (ii) any funding from an affiliate of the Company with the term affiliate defined in accordance with the definition used by the U.S. Securities and Exchange Commission and (iii) funding of any other type from any other source or funds provider. To avoid any doubt, any funding the Company receives under its Standby Equity Purchase Agreement with an affiliate of Yorkville Global Advisors (the “SEPA”) shall count as Qualified Funding.

(b)           Equity Treatment.

(i)            The Company shall also grant you on the Separation Date an option to purchase 185,000 shares of common stock (the “Equity Award”). Notwithstanding the terms and conditions of the Equity Documents, the Equity Award shall be for a term of 10 years from the date of grant and the exercise price shall be the closing price of the common stock on the Separation Date. The Company shall use commercially reasonable efforts to register the Equity Award on a Registration Statement on Form S-8 as soon as practicable but in no event later than December 31, 2026. The Equity Award will vest and become exercisable in equal monthly installments over the 12 months following the Separation Date, subject to acceleration: (i) in full upon a Sale Event (as defined in the Equity Documents) or the achievement of the $10 Million Financing; or (ii) as to 50% of the Equity Award upon the achievement of the $5 Million Financing. The Equity Award otherwise will be subject to the applicable Equity Documents.

(ii)           Notwithstanding anything to the contrary in the Equity Documents, as of the Effective Date, subject to your compliance with this Agreement, all outstanding equity awards held by you shall become fully vested and the exercise period for any such equity awards, as applicable, shall be extended through the end of the original full term of such awards set forth in the applicable Equity Documents.

(c)           Health Benefits. If you elect and remain eligible for COBRA continuation coverage, the Company shall pay in full twelve (12) months of COBRA premiums until the earlier of the 12-month anniversary of the Separation Date, your eligibility for health insurance from a subsequent employer or the end of your eligibility under COBRA for such continuation coverage. In the alternative, the Company shall elect to pay your portion of Medicare premiums in the event that you do not elect or are not eligible for COBRA continuation coverage. You agree to inform the Company promptly upon your eligibility for group health insurance from a subsequent employer, and you agree to respond promptly to the Company’s reasonable COBRA-related inquiries.

2.            Transitional Services

You agree to provide transitional services (the “Transitional Services”) (i) for up to 20 hours during September 2026 (the “Transitional Period”) for hours reasonably agreed by you and the Company with no fee payable to you; and (ii) for any hours thereafter mutually agreed upon by you and the Company at an hourly rate of $350. In the event you provide Transitional Services as set forth above, the Company shall not deem your Services as substandard in any way except in the event of gross negligence or fraud and shall not attempt to argue that the quality of Transitional Services that you provide in any way (except in the event of gross negligence or fraud) constitutes a breach of this Agreement permitting the Company to claim a right to reduce any amounts owed you hereunder. For clarity, your provision of Transitional Services shall not constitute a service relationship for the purpose of any compensation or benefits, including without limitation under the equity incentive plans and Equity Documents. Notwithstanding the foregoing, the Company may terminate the Transitional Period at any time if you commit gross negligence or fraud or materially breach the Ongoing Obligations or this Agreement. The Company further agrees and acknowledges that any services you may provide to any third parties during the Transitional Period do not represent a conflict with this Agreement or your provision of Transitional Services to the Company. To the extent you provide Transitional Services, the Company shall provide you with all information and materials reasonably required, in the Company’s judgment, for you to perform the Transitional Services.

3.            Resignations from Other Positions; Transition of Information and Access

In connection with the ending of your employment, you hereby (i) resign from any and all Company positions, including, without implication of limitation, as Vice President of Administration, Chief Financial Officer, Secretary and director of the Company, as trustee or other officer, or other positions you occupy, or may be deemed to occupy, at the Company, or any of its subsidiaries or affiliates, in each case effective as of the Separation Date; (ii) agree to execute such documentation as the Company or its applicable subsidiary or affiliate reasonably requires to effectuate such resignations; and (iii) take such steps as the Company (or its applicable subsidiary or affiliate) reasonably requests to ensure the transition of any account access, systems access, password access, customer access, confidential information, Company property, customer information or customer relationships to the Company or its applicable subsidiary or affiliate. You acknowledge and agree that your resignations described in this section shall be effective as of the date of this Agreement and shall not be subject to the Revocation Period (as defined below) or otherwise revocable.

4.            Mutual Release of Claims

In consideration for, among other terms, your eligibility for the consideration described in this Agreement, you, on behalf of yourself and your heirs, administrators, representatives, successors and assigns (together with you, the “Employee Releasors”) voluntarily release and forever discharge the Company, its affiliated and related entities, its and their respective predecessors, successors and assigns, its and their respective employee benefit plans and fiduciaries of such plans, and the current and former employees, officers, directors, shareholders, interest holders, managers, members, partners, investors, attorneys, accountants and agents of each of the foregoing in their official and personal capacities (collectively referred to as the “Company Releasees”) generally from all claims, demands, debts, damages and liabilities of every name and nature, known or unknown (“Claims”) that, as of the date when you sign this Agreement, you or any other Employee Releasor have, ever had, now claim to have or ever claimed to have had against any or all of the Company Releasees. This release includes, without limitation, all Claims:

provided, however, that this release shall not affect your rights under this Agreement, any indemnification rights you have under the Company’s applicable indemnification agreement, charter, and/or bylaws, or your vested rights under (and subject to) the Equity Documents.

You acknowledge and represent that, except as expressly provided in this Agreement including but not limited to payment of the Accrued Obligations as defined herein, the Company has paid or provided all salary, wages, bonuses, accrued vacation/paid time off, premiums, leaves, housing allowances, relocation costs, interest, severance, outplacement costs, fees, reimbursable expenses, commissions, stock, stock options, vesting, and any and all other benefits and compensation due to you except that the Company shall reimburse you for $12,500 for legal fees and expenses incurred in connection with the negotiation of this Agreement at the same time as the Severance Payment under Section 1(a)(i). You specifically represent that you are not due to receive any commissions or other incentive compensation from the Company except as provided in this Agreement.

You agree not to accept damages of any nature, other equitable or legal remedies for your own benefit or attorney’s fees or costs from any of the Company Releasees with respect to any Claim released by this Agreement. As a material inducement to the Company to enter into this Agreement, you represent that you have not assigned any Claim to any third party.

The Company, its affiliated and related entities and subsidiaries, its and their respective predecessors, successors and assigns, and the current and former employees, officers, directors, shareholders, interest holders, managers, members, partners, investors, attorneys, accountants and agents of each of the foregoing in their official capacities (the “Company Releasors”) voluntarily release and forever discharge you on behalf of yourself and your heirs, administrators, representatives, successors and assigns (the “Employee Releasees”) generally from all claims, demands, debts, damages and liabilities of every name and nature, known or unknown (“Claims”) that, as of the date of the execution of this Agreement, the Company Releasors have, ever had, now claim to have or ever claimed to have had against any or all of the Employee Releasees, provided, however, that this release shall not affect the Company Releasors’ rights under this Agreement, any indemnification rights Company Releasors’ have under the Company’s applicable indemnification agreement, charter, and/or bylaws, or Company Releasors’ rights under (and subject to) the Equity Documents.

The Company Releasors agree not to accept damages of any nature, other equitable or legal remedies for their own benefit, or attorney’s fees or costs from any of the Employee Releasees with respect to any Claim released by this Agreement. As a material inducement to the Company entering into this Agreement, the Company Releasors represent that they have not assigned any Claim to any third party.

You shall not dispose of Company property (including information, documents, computerized data and any copies made of any of the foregoing (“Documents”)), without written authorization. The Company shall permit you to retain the Company Lenovo laptop with asset tag number 1003, provided you first furnish the laptop to the Company to allow the Company to wipe the laptop of all Company data. Notwithstanding the foregoing, you agree to return to the Company all Company property, including, without limitation, keys and access cards, credit cards, files and any Documents containing information concerning the Company, its business or its business relationships (in the latter two cases, actual or prospective) and any information about the Company’s commercial and technical strategies and mechanics associated with implementing those strategies, on or before the fifteenth (15^th) day following the Separation Date. After returning all Documents and Company property, you commit to deleting and finally purging any duplicates of files or documents that may contain Company information from any non-Company computer or other device that remains your property. In the event that you discover that you continue to retain any such property, you shall return it to the Company immediately.

Subject to the Protected Activities section below, you agree not to make any oral or written disparaging statements (including through social media) concerning the Company or any of its affiliates or current or former officers, directors, shareholders, employees or agents. You further agree not to take any actions or conduct yourself in any way that would reasonably be expected to affect adversely the reputation or goodwill of the Company or any of its affiliates or any of its current or former officers, members, directors, shareholders, employees or agents. These non-disparagement obligations shall not in any way affect your obligation to testify truthfully in any legal proceeding. The Company‘s C-level officers and its current directors shall not: (i) make any oral or written disparaging statements (including through social media) concerning you; or (ii) take any actions or conduct themselves in any way that would reasonably be expected to affect adversely your reputation or goodwill.

7.            Announcement of Transition

You agree to assist the Company, at the Company’s reasonable request, with the press release announcing your resignation. The Company will submit the press release for your review and you agree to respond promptly with any comments you may have, which will be considered in good faith by the Company.

8.            Confidentiality of Agreement-Related Information; Other Obligations

Subject to the Protected Activities section below, you agree, to the fullest extent permitted by law, to keep all Agreement-Related Information completely confidential. “Agreement-Related Information” means the negotiations leading to this Agreement and the terms of this Agreement. Notwithstanding the foregoing, you may disclose Agreement-Related Information to your spouse, your family, your attorney and your financial advisors, and to them only provided that they first agree for the benefit of the Company to keep Agreement-Related Information confidential. You represent that during the period since you received the first draft of this Agreement, you have not made any disclosures that would have been contrary to the foregoing obligation if it had then been in effect. Nothing in this section shall be construed to prevent you from disclosing Agreement-Related Information to the extent required by a lawfully issued subpoena or duly issued court order; provided that you provide the Company with advance written notice and a reasonable opportunity to contest such subpoena or court order. You agree to notify future employers of your Ongoing Obligations.

9.            Protected Activities

Nothing contained in this Agreement or in any other agreement with the Company limits your ability to: (i) file a charge or complaint with any federal, state or local governmental agency or commission, including without limitation the Equal Employment Opportunity Commission, the National Labor Relations Board or the Securities and Exchange Commission (a “Government Agency”); (ii) communicate with any Government Agency or otherwise participate in any investigation or proceeding that may be conducted by any Government Agency; (iii) exercise any rights you may have under Section 7 of the National Labor Relations Act, including any rights you may have under such provision to assist co-workers with or discuss any employment issue, dispute or term or condition of employment as part of engaging in concerted activities for the purpose of mutual aid or protection; (iv) discuss or disclose information about unlawful acts in the workplace, such as harassment or discrimination or any other conduct that you have reason to believe is unlawful; or (v) testify truthfully in a legal proceeding, in any event with or without notice to or approval of the Company so long as such communications and disclosures are consistent with applicable law and the information disclosure was not obtained through a communication that was subject to the attorney client privilege (unless disclosure of that information would otherwise be permitted consistent with such privilege). If you file any charge or complaint with any Government Agency and if the Government Agency pursues any claim on your behalf, or if any other third party pursues any claim on your behalf, you waive any right to monetary or other individualized relief (either individually or as part of any collective or class action) but the Company will not limit any right you may have to receive an award by an order of a Government Agency pursuant to the whistleblower provisions of any applicable law or regulation for providing information to the SEC or any other Government Agency.

10.          Defend Trade Secrets Act Notice

You understand that pursuant to the Defend Trade Secrets Act of 2016, you shall not be held criminally or civilly liable under any federal or state trade secret law for the disclosure of a trade secret that (A) is made (i) in confidence to a federal, state, or local government official, either directly or indirectly, or to an attorney; and (ii) solely for the purpose of reporting or investigating a suspected violation of law; or (B) is made in a complaint or other document filed in a lawsuit or other proceeding, if such filing is made under seal.

11.          Other Provisions

(a)           Termination and Return of Payments. If you breach any of your material obligations under this Agreement or the Ongoing Obligations, in addition to any other legal or equitable remedies it may have for such breach, and notwithstanding anything to the contrary in any agreement between you and the Company, the Company shall have the right to terminate and/or enforce the return of its non-wage payments to you or for your benefit under this Agreement and terminate any extended exercise period for your equity rights. Such remedies in the event of your breach will not affect your continuing obligations under this Agreement.

(b)           Enforceability. If any portion or provision of this Agreement (including, without limitation, any portion or provision of any section of this Agreement) shall to any extent be declared illegal or unenforceable by a court of competent jurisdiction, then the remainder of this Agreement, or the application of such portion or provision in circumstances other than those as to which it is so declared illegal or unenforceable, shall not be affected thereby, and each portion and provision of this Agreement shall be valid and enforceable to the fullest extent permitted by law.

(c)           Waiver; Absence of Reliance. No waiver of any provision of this Agreement shall be effective unless made in writing and signed by the waiving party. The failure of a party to require the performance of any term or obligation of this Agreement, or the waiver by a party of any breach of this Agreement, shall not prevent any subsequent enforcement of such term or obligation or be deemed a waiver of any subsequent breach. In signing this Agreement, you are not relying upon any promises or representations made by anyone at or on behalf of the Company.

(d)           Jurisdiction; Governing Law; Interpretation. Except as expressly otherwise provided in the Equity Documents: (i) you and the Company hereby agree that the state and federal courts of Massachusetts located in Boston shall have the exclusive jurisdiction to consider any matters related to this Agreement, including without limitation any claim of a violation of this Agreement; and (ii) with respect to any such court action, you and the Company submit to the jurisdiction of such courts and you and the Company acknowledge that venue in such courts is proper; and (iii) this Agreement shall be interpreted and enforced under the laws of Massachusetts, without regard to conflict of law principles. You and the Company waive any right to a jury with respect to any dispute between you.

(e)           Entire Agreement. This Agreement, the Ongoing Obligations (which are incorporated herein by reference), the Equity Documents, and any indemnification rights you have under the Company’s applicable indemnification agreement, charter, and/or bylaws constitute the entire agreement between you and the Company and supersede any previous agreements, understandings or communications between you and the Company.

(f)            Time for Consideration; Effective Date. You acknowledge that the Company proposed an agreement to you on August 20, 2026 (the “Initial Proposal”) and that you have been given the opportunity to consider this Agreement for twenty-one (21) days from the date of the Initial Proposal (the “Consideration Period”). You agree that any edits since your receipt of the first draft of the Agreement do not restart the Consideration Period. You acknowledge that the above release of claims expressly includes without limitation claims under the Age Discrimination in Employment Act. You acknowledge that you consulted with an attorney before signing this Agreement. To accept this Agreement, you must return a signed original or a signed PDF copy of this Agreement so that it is received by the undersigned at or before the expiration of the Consideration Period. If you sign this Agreement before the end of the Consideration Period, you acknowledge by signing this Agreement that such decision was entirely voluntary and that you had the opportunity to consider this Agreement for the entire Consideration Period. For the period of seven (7) days from the date when you sign this Agreement (the “Revocation Period”), you have the right to revoke this Agreement by written notice to the undersigned. For such a revocation to be effective, it must be delivered so that it is received by the undersigned at or before the expiration of the Revocation Period. This Agreement shall not become effective or enforceable during the Revocation Period. It will become effective on the day after the Revocation Period ends (the “Effective Date”).

(g)            Counterparts. This Agreement may be executed in separate counterparts. When all counterparts are signed, including by electronic means other than facsimile, they shall be treated together as one and the same document.

Please indicate your agreement to the terms of this Agreement by signing and returning to the undersigned the original or a PDF copy of this letter within the time period set forth above.

Very truly yours,

TransCode Therapeutics, Inc.

This is a legal document. Your signature will commit you to its terms. By signing below, you acknowledge that you have carefully read and fully understand all of the provisions of this Agreement and that you are knowingly and voluntarily entering into this Agreement.