Highly crystalline platinum nanoclusters, prepared by the pulse electrochemical deposition (PED) method, onto graphene sheets, served as a catalyst electrode for proton exchange membrane fuel cell was investigated. The ratio of current-on to current-off time appears to be a crucial factor in affecting the surface density and the crystalline structure of Pt clusters. The linear relation between Pt loading and current-off time confirms that ionic diffusion acts as a rate-determining step in the PED process. The electrochemical performance of Pt catalyst electrodes was characterized by electrochemical impedance spectroscopy and the single cell test at 30–75°C. The ratio of Pt (111) plane in the cluster showed a positive effect on the improvement of equivalent series resistance and power density. The single cell equipped with the Pt catalyst electrode delivered the lowest inner resistance of 1.07Ω and the highest power density of 1.48kWg−1.