First Amendment to Note Purchase Agreement, dated as of August 4, 2023

Exhibit 10.1

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Execution Version

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FIRST AMENDMENT TO

NOTE PURCHASE AGREEMENT

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This FIRST AMENDMENT TO NOTE PURCHASE AGREEMENT, dated as of August 4, 2023 (“Amendment”), is made by and among Milestone Pharmaceuticals Inc., a corporation existing under the Business Corporations Act (Québec) (the “Company”), the Purchasers (defined below), RTW Investments, LP, as agent for the Purchasers (in such capacity, the “Principal Purchaser”) and acknowledged and agreed by Acquiom Agency Services LLC, as collateral agent for the Purchasers (in such capacity, the “Collateral Agent”). Capitalized terms used herein, but not otherwise defined herein shall have the respective meanings set forth in the Note Purchase Agreement (defined below).

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WITNESSETH:

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WHEREAS, the Company entered into the Note Purchase Agreement, dated as of March 27, 2023 (the “Note Purchase Agreement”), with the purchasers from time to time party thereto (each, a “Purchaser”, and collectively, the “Purchasers”), the Principal Purchaser, and the Collateral Agent, pursuant to which the Company has issued $50,000,000 aggregate principal amount of its 6.0% Convertible Senior Secured Notes due March 31, 2029 (each as amended, restated, supplemented or otherwise modified from time to time, the “Notes”); and

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WHEREAS, in accordance with Section 13.6 of the Note Purchase Agreement, the Company, the Purchasers, and the Principal Purchaser have agreed that Section 7 of the Note Purchase Agreement be amended.

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NOW, THEREFORE, in consideration of the covenants and agreements contained herein, as well as other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

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SECTION 1. Amendments. Effective as of the Amendment Effective Date (as defined below):

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(a) Section 1.1 is amended by adding the following term with the following meaning:

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“Grantor” means the Company and the Guarantors.

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(b) Section 7.1 is amended by adding a Section 7.1(d) with language as follows:

(d) enter into any control agreement, blocked account, lockbox or similar arrangement with the applicable depository institution or intermediary, the applicable Grantor and any secured party (other than the Collateral Agent) with respect to any deposit accounts securities accounts and commodities accounts held or maintained in Canada (excluding any Excluded Account (as defined in the Guarantee and Collateral Agreement)), other than in connection with Indebtedness permitted under Section 7.1(b)(v) hereof, provided that such

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Indebtedness will be subject to subject to customary first lien/second lien intercreditor arrangements.

(c) The requirement to deliver control agreements for any Closing Date Account held in Canada pursuant to paragraph 2 on Schedule C to the Note Purchase Agreement is hereby removed.

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SECTION 2. Conditions to Amendment Effectiveness. The effectiveness of this Amendment is subject to satisfaction of the following conditions precedent (the date of such satisfaction being the “Amendment Effective Date”):

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(a)(i) the Company shall have executed and delivered a counterpart of this Amendment to each Purchaser and the Principal Purchaser and (ii) each Purchaser and the Principal Purchaser shall have executed and delivered counterparts of this Amendment to the Company; and

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(b) no Event of Default shall have occurred and be continuing before and immediately after giving effect to this Amendment.

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SECTION 4. Representations and Warranties. The Company hereby represents and warrants to each Purchaser and the Principal Purchaser, on and as of the Amendment Effective Date, that:

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(a)  The Company has all requisite corporate power and has taken all necessary corporate action required for the due authorization, execution, delivery and performance by the Company of this Amendment and the other Note Documents and the consummation of the transactions contemplated hereby and thereby. The execution, delivery and performance by the Company of this Amendment and the consummation by the Company of the transactions contemplated hereby, have been duly authorized by the Board of Directors and no further consent or authorization of the Company, the Board of Directors or its shareholders is required. This Amendment has been duly executed and delivered by the Company, and the other instruments referred to herein, including the Note Documents, to which it is a party and any Note Document to which it is a party will be duly executed and delivered by the Company, and each such instrument or Note Document constitutes or will constitute a legal, valid and binding obligation of the Company enforceable against it in accordance with its terms, except to the extent that enforceability may be limited by bankruptcy, insolvency, reorganization, moratorium, fraudulent conveyance, and any other laws of general application affecting enforcement of creditors’ rights generally, and as limited by laws relating to the availability of specific performance, injunctive relief, or other equitable remedies.

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SECTION 5. Effects on the Note Purchase Agreement.

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(a)  On and after the Amendment Effective Date, each reference in the Note Purchase Agreement or any Note Document to the Note Purchase Agreement shall mean and be a reference to the Note Purchase Agreement as amended by this Amendment, and each reference in the Note Purchase Agreement to “this Agreement,” “hereunder,” “hereof” or words of like import shall mean and be a reference to the Note Purchase Agreement as amended by this Amendment.

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(b)  This Amendment does not constitute a novation or termination of the obligations under the Note Purchase Agreement; and except as specifically amended or otherwise modified hereby, all of the Note Documents shall continue to be in full force and effect and are hereby in all respects ratified and confirmed and no provision of the Note Purchase Agreement (including the definition of Final Availability Date therein) or the other Note Documents are amended in any way other than as expressly provided herein.

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(c)  Except as expressly set forth herein, this Amendment shall not by implication or otherwise limit, impair, constitute a waiver of or otherwise affect the rights and remedies of the Purchasers, Principal Purchaser or the Company under any Note Document.

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(d)  This Amendment shall constitute a Note Document for all purposes of the Note Purchase Agreement and the other Note Documents.

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SECTION 6. Miscellaneous.

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(a)Sections 13.2, 13.8, 13.9 of the Note Purchase Agreement are hereby incorporated herein by reference mutatis mutandis.

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(b)The undersigned Purchasers, constituting all of the Purchasers, hereby direct the Collateral Agent to execute this Amendment.

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[Remainder of page intentionally left blank; signature pages follow.]

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IN WITNESS WHEREOF, the parties hereto have caused their duly authorized officers to execute and deliver this Amendment as of the date first above written.

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This Amendment is hereby
accepted and agreed to as
of the date hereof.

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