EX-5.1

Exhibit 5.1

[Letterhead of Morrison & Foerster LLP]

June 21, 2024

Board of Directors

Crinetics Pharmaceuticals, Inc.

6055 Lusk Boulevard

San Diego, CA 92121

Re: Crinetics Pharmaceuticals, Inc. — At the Market Offering of Shares of Common Stock having an Aggregate Offering Price of up to $350,000,000

Ladies and Gentlemen:

We have acted as counsel to Crinetics Pharmaceuticals, Inc., a Delaware corporation (the “Company”), in connection with the sale and issuance by the Company from time to time of shares of its common stock, $0.001 par value per share (the “Common Stock”), having an aggregate offering price of up to $350,000,000 (collectively, the “Shares”) pursuant to (i) the terms of the Sales Agreement, dated June 21, 2024 (the “Sales Agreement”), among the Company, Leerink Partners LLC and Cantor Fitzgerald & Co. (together, the “Agents”), and (ii) the Registration Statement on Form S-3 (Registration No. 333-280407) (the “Registration Statement”), the related Prospectus dated June 21, 2024 (the “Base Prospectus”) and the related Prospectus Supplement dated June 21, 2024 (together with the Base Prospectus, the “Prospectus”), filed with the Securities and Exchange Commission (the “Commission”) under the Securities Act of 1933, as amended (the “Securities Act”). The Shares will be issued from time to time in public offerings at market or negotiated prices under Rule 415 of the Securities Act.

This opinion is being furnished in connection with the requirements of Item 601(b)(5) of Regulation S-K under the Securities Act, and no opinion is expressed herein as to any matter pertaining to the contents of the Registration Statement or the Prospectus, other than as expressly stated herein with respect to the Shares.

As counsel for the Company, we have examined the Registration Statement, the Sales Agreement, the Company’s Amended and Restated Certificate of Incorporation (the “Charter”), the Company’s Amended and Restated Bylaws and originals or copies, certified or otherwise identified to our satisfaction, of such agreements, instruments, documents, certificates and records as we have deemed relevant and necessary for the basis of our opinions hereinafter expressed, and we are familiar with the proceedings taken and proposed to be taken by the Company in connection with the authorization, issuance and sale of the Shares. In such examination, we have assumed: (i) the authenticity of original documents and the genuineness of all signatures; (ii) the conformity to the originals of all documents submitted to us as copies; (iii) the truth, accuracy and completeness of the information, representations and warranties contained in the agreements, instruments, documents, certificates and records that we have reviewed; and (iv) the legal capacity of all natural persons. As to all matters of fact, we have relied on the representations and statements of fact made in the documents so reviewed, and we have not independently established or verified the facts so relied on. We have further assumed that, upon the issuance of any of the Shares, the total number of shares of Common Stock issued and outstanding will not exceed the total number of shares of Common Stock that the Company is then authorized to issue under the Charter. This opinion letter is given, and all statements herein are made, in the context of the foregoing.

Based upon, subject to and limited by the foregoing, it is our opinion that, upon issuance, delivery and payment therefor in the manner contemplated by the Registration Statement, the Prospectus, the Sales Agreement and resolutions of the Board of Directors of the Company or a duly authorized committee thereof, the Shares will be validly issued, fully paid and nonassessable.

This opinion letter is based as to matters of law solely on the Delaware General Corporation Law, as amended. We express no opinion herein as to any other laws, statutes, ordinances, rules or regulations. As used herein, the term “Delaware General Corporation Law, as amended” includes the statutory provisions contained therein, all applicable provisions of the Delaware Constitution and reported judicial decisions interpreting these laws.