The aim of this study is to investigate the effects of the separator thickness on not only the heat and mass transfer characteristics, but also the power generation characteristics of a polymer electrolyte membrane fuel cell (PEMFC) with a thin polymer electrolyte membrane (PEM) and thin gas diffusion layer (GDL) operated at higher temperatures of 363 and 373 K. The in-plane temperature distributions on the back of the separator at the anode and cathode, which are the opposite sides to the GDL, are measured using a thermograph at various initial cell temperatures (Tinit), relative humidity (RH) levels, and supply gas flow rates. The total voltage corresponding to the load current is measured in order to evaluate the performance of the PEMFC. As a result, it is revealed that the effect of the RH on the power generation characteristics is more significant when the separator thickness decreases. It is revealed that the power generation performance obtained at high current densities decreases with the increase in Tinit with thinner separator thicknesses. According to the investigation of the in-plane temperature distribution, it is clarified that the temperature decreases at corner positions in the separator with the separator thickness of 2.0 mm, while the temperature gradually increases along with the gas flow with separator thicknesses of 1.5 mm and 1.0 mm.