Maze Therapeutics, Inc. 5,540,000Shares of Common Stock Pre-Funded Warrants to Purchase 850,000 Shares of Common Stock We are offering 5,540,000shares of our common stock and, in lieu of common stock to certain investors that so choose, pre-funded warrants to purchaseshares of common stock pursuant to this prospectus supplement and the accompanying prospectus. The purchase price of each pre-funded warrantequals the price per share at which shares of our common stock are being sold in this offering, minus $0.001, which is the exercise price of eachpre-funded warrant. This prospectus supplement also relates to the offering of the shares of our common stock issuable upon exercise of such pre-fundedwarrants. Our common stock is listed on The Nasdaq Global Market under the symbol “MAZE.” The last reported sale price of our common stock on The NasdaqGlobal Market on April21, 2026, was $25.69per share. There is no established public trading market for the pre-funded warrants, and we do not expecta market to develop. In addition, we do not intend to apply for a listing of the pre-funded warrants on The Nasdaq Global Market, any other nationalsecurities exchange or any other nationally recognized trading system. We are an “emerging growth company” as those terms are defined under federal securities laws and, as such, we have elected to comply with certainreduced public company reporting requirements for this prospectus and may elect to do so in future filings. Investing in our securities involves a high degree of risk. See the section titled “Riskfactors” beginning on page S-6 ofthis prospectus supplement. Neither the Securities and Exchange Commission nor any other regulatory body has approved or disapproved of these securities or passed onthe adequacy or accuracy of this prospectus. Any representation to the contrary is a criminal offense. Delivery of the shares of common stock and pre-funded warrants is expected to be made on or about April23, 2026. LeerinkPartners The date of this prospectus supplement is April21, 2026. Table of Contents TABLE OF CONTENTS Prospectus Supplement About this prospectus supplementProspectus supplement summaryThe offeringRisk factorsSpecial note regarding forward-looking statementsWhere you can find more informationIncorporation of information by referenceUse of proceedsDividend policyDilutionDescription ofpre-funded warrantsMaterial United States federal income tax consequences for investors in our common stock andpre-funded warrantsUnderwritingLegal mattersExperts Prospectus About this prospectusProspectus summaryRisk factorsSpecial note regarding forward-looking statementsWhere you can find more informationIncorporation of information by referenceUse of proceedsSelling securityholders Plan of distribution Description of capital stockDescription of debt securitiesDescription of warrantsDescription of subscription rightsDescription of unitsLegal mattersExperts Table of Contents ABOUT THIS PROSPECTUS SUPPLEMENT This prospectus supplement and the accompanying prospectus are part of an automatic shelf registration statement on Form S-3ASR that we filed withthe Securities and Exchange Commission (SEC) as a “well-known seasoned issuer” as defined in Rule 405 under the Securities Act of 1933, as amended(Securities Act). Under this shelf registration process, we may from time to time sell any combination of the securities described in the accompanyingbase prospectus in one or more offerings and selling stockholders may, from time to time, sell shares of our common stock from time to time in one ormore offerings as described in the accompanying base prospectus. We provide information to you about this offering of our securities in two separate documents that are bound together: (1)this prospectus supplement,which describes the specific details regarding this offering; and (2)the accompanying base prospectus, which provides general information, some ofwhich may not apply to this offering. Generally, when we refer to this “prospectus,” we are referring to both parts combined. To the extent there is aconflict between the information contained in this prospectus supplement, on the one hand, and the information contained in the accompanying baseprospectus that was filed with the SEC before the date of this prospectus supplement, on the other hand, you should rely on the information in thisprospectus supplement; provided that, if any statement in one of these documents is inconsistent with a statement in another document having a laterdate—for example, a document incorporated by reference in this prospectus supplement—the statement in the document having the later date modifiesor supersedes the earlier statement. This prospectus supplement, the accompanying prospectus and the documents incorporated into each by reference include important information aboutus, the securities being offered and other information you should know before investing in our securities. You should als