Common Stock We are offering 7,620,000 shares of our common stock in this offering. Our common stock is listed on The Nasdaq Global Select Market under the symbol “CRNX.” On January6, 2026, the last reported sale price of ourcommon stock on The Nasdaq Global Select Market was $45.95 per share. (1)See “Underwriting” for additional information regarding total underwriters’ compensation, including expenses for which we have agreed toreimburse the underwriters. We have granted the underwriters an option for a period of 30 days to purchase up to an additional 1,143,000 shares of our common stock on the sameterms as set forth above. Investing in our common stock involves risks. See “Risk Factors” beginning on pageS-7 of this prospectus supplementand the documents incorporated by reference into this prospectus supplement. Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or passedupon the adequacy or accuracy of this prospectus supplement or the accompanying prospectus. Any representation to the contrary is a criminaloffense. The underwriters expect to deliver the shares of common stock to purchasers on or about January 8, 2026. Cantor Piper Sandler Leerink Partners J.P. Morgan Prospectus Supplement About this Prospectus SupplementProspectus Supplement Summary Page12241 About this ProspectusWhere You Can Find More InformationInformation Incorporated by ReferenceThe CompanyRisk FactorsCautionary Note Regarding Forward-Looking StatementsUse of ProceedsDescription of Capital StockDescription of Debt SecuritiesDescription of WarrantsDescription of UnitsGlobal SecuritiesSelling SecurityholdersPlan of DistributionLegal MattersExperts Neither we nor any of the underwriters have authorized anyone to provide information different from that contained in this prospectus supplement.When you make a decision about whether to invest in our common stock, you should not rely upon any information other than the information in thisprospectus supplement. Neither the delivery of this prospectus supplement nor the sale of shares of our common stock means that information contained Table of Contents ABOUT THIS PROSPECTUS SUPPLEMENT This prospectus supplement and the accompanying prospectus dated June21, 2024 are part of a registration statement that we filed with the Securitiesand Exchange Commission (the “SEC”) as a “well-known seasoned issuer,” as defined in Rule 405 under the Securities Act of 1933, as amended(“Securities Act”), utilizing a “shelf” registration process. This prospectus supplement and the accompanying prospectus relate to the offer by us ofshares of our common stock to certain investors. We provide information to you about this offering of shares of our common stock in two separatedocuments that are bound together: (1)this prospectus supplement, which describes the specific details regarding this offering; and (2)theaccompanying prospectus, which provides general information, some of which may not apply to this offering. Generally, when we refer to this“prospectus,” we are referring to both documents combined. If information in this prospectus supplement is inconsistent with the accompanyingprospectus, you should rely on this prospectus supplement. However, if any statement in one of these documents is inconsistent with a statement inanother document having a later date—for example, a document incorporated by reference in this prospectus supplement or the accompanying You should rely only on information contained in or incorporated by reference into this prospectus supplement and the accompanying prospectus, andany free writing prospectus that we may authorize for us in connection with this offering. We have not, and the underwriters have not, authorized anyoneto provide you with information that is different. We are not, and the underwriters are not, making an offer to sell these securities in any jurisdictionwhere the offer or sale is not permitted or in which the person making that offer or solicitation is not qualified to do so or to anyone to whom it isunlawful to make an offer or solicitation. The information contained in this prospectus supplement, the accompanying prospectus, the documents and In this prospectus supplement, unless the context otherwise indicates, the terms “Crinetics,” the “Company,” “we,” “our” and “us” or similar terms referto Crinetics Pharmaceuticals, Inc., including its subsidiary. We use our registered trademark Crinetics and our pending trademark PALSONIFY™in this prospectus supplement. All other trademarks, trade namesand service marks appearing in this prospectus supplement or the documents incorporated by reference herein are the property of their respectiveowners. Use or display by us of other parties’ trademarks, trade dress or products is not intended to and does not imply a relationship with, orendorsements or sponsorship of, us by the trademark or trade dress owner. Solely for