We studied the effects of the alkynyl and thiolate ligands (L) on the catalytic activities of Au25(L)18 and PtAu24(L)18 for the hydrogen evolution reaction (HER): the ligands used were C≡CArF (ArF = 3,5-bis(trifluoromethyl)-phenyl) and SC2H4Ph. The onset potential for Au25(C≡CArF)18 was shifted to the positive side by ∼70 mV with respect to that for Au25(SC2H4Ph)18, indicating that the HER activity of the pure Au13 core was significantly enhanced when protected by alkynyl ligands. This remarkable ligand effect was explained by the acceleration of the protonation step to the more negatively charged Au25(C≡CArF)18 than the less negatively charged Au25(SC2H4Ph)18. In contrast, the HER activities of the doped PtAu24(C≡CArF)18 and PtAu24(SC2H4Ph)18 were comparable. The negligible ligand effect on the activity of the Pt@Au12 core was ascribed to the change in the rate-determining step from the protonation step to the reductive regeneration step of the catalysts.