Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We consent to the reference to our firm under the caption "Experts" in this Registration Statement (Form S-3) and related Prospectus of Protagonist Therapeutics, Inc. for the registration of common stock, preferred stock, debt securities, warrants and/or units and to the incorporation by reference therein of our reports dated February 21, 2025, with respect to the consolidated financial statements of Protagonist Therapeutics, Inc., and the effectiveness of internal control over financial reporting of Protagonist Therapeutics, 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 Mateo, California

August 6, 2025