Given the synergetic properties of different metal species, bimetallic nanoparticles are of immense scientific interest and technological importance in the field of catalysis. A peptide‐based method represents a new avenue to fabricate bimetallic nanocatalysts with a controllable size, shape, composition, and subtle surface microstructure. However, the electrocatalytic abilities of these peptide‐based bimetallic nanoparticles remain largely unexplored. Herein, we employed the peptide sequence FlgA3 to fabricate a series of AuPd alloys that were used as catalysts for the oxygen reduction reaction (ORR). Among the samples tested, Au33Pd67 exhibited the best activity, evidenced by the most positive onset potential and the largest diffusion‐limited current. Notably, the ORR activity of Au33Pd67 was comparable with that of commercial Pt/C, and the long‐term durability was significantly superior to that of Pt/C. A peptide‐enabled approach might pave the way for the fabrication of bimetallic nanomaterials with enhanced electrocatalytic properties under mild conditions.