Exhibit 23.1

Consent of Independent Registered Public Accounting Firm

We consent to the reference to our firm under the caption “Experts” in the Registration Statement (Form S-3) and related Prospectus of Assembly Biosciences, Inc. for the registration of common stock, preferred stock, debt securities, warrants, subscription rights and units, and to the incorporation by reference therein of our report dated March 20, 2025, with respect to the consolidated financial statements of Assembly Biosciences, Inc., included in its Annual Report (Form 10-K) for the year ended December 31, 2024, filed with the Securities and Exchange Commission.

/s/ Ernst & Young LLP

San Jose, California

March 20, 2025