Although Pt is a widely adopted commercial catalyst for the hydrogen evolution reaction (HER), its practical application is greatly limited by its prohibitive cost and high energy barrier for H2O dissociation in alkaline media. Herein, an ultrafine Pt-based catalyst decorated with oxygenophilic Ni-sites is rationally designed and successfully synthesized with Pt5(GS)10 (HGS = l-reduced glutathione) nanocluster precursor. The optimized Ni-decorated Pt catalyst (Ni-Pt-C-500) with ultrafine nanoparticles (about 1.6 nm) exhibits a low overpotential (14.0 mV) at 10 mA cm−2 and a mild Tafel slope of 20.8 mV dec−1 in the HER, which is superior to its undecorated counterpart (Pt-C-500), the commercial 20 wt% Pt/C catalyst and most of the previously reported Pt-based electrocatalysts. Experimental observations and theoretical calculations indicate that H2O could be spontaneously adsorbed to Ni-sites of the Ni-Pt-C-500 catalyst. Mechanistic studies reveal that Ni-sites promote HER by accelerating the kinetic of H2O cleavage and optimizing the electronic structure of Pt. This work paves a new avenue for designing other ultrafine hybrid electrocatalysts based on metal nanoclusters to enhance catalytic reaction kinetics.