Considering the application of the polymer electrolyte membrane fuel cell (PEMFC), the separator thickness plays a significant role to determine the weight, the volume and the costs of the PEMFC. In addition, thermal management, i.e., temperature distribution is also important for the PEMFC system to obtain higher performance. However, there were few reports investigating the relation between the temperature profile and the power generation characteristics e.g., current density distribution of PEMFC operated at higher temperature (HT-PEMFC). This paper aims to study the impact of separator thickness on the temperature profile and the current density profile of HT-PEMFC. The impact of separator thickness on the gases i.e., H2, O2 profile of HT-PEMFC numerically was also studied using CFD software COMSOL Multiphysics in the paper. In the study, the operating temperature and the relative humidity (RH) of supply gas were varied with the separator thickness of 2.0 mm, 1.5 mm and 1.0 mm, respectively. The study revealed that the optimum thickness was 2.0 mm to realize higher power generation of HT-PEMFC. The heat capacity of the separator thickness of 2.0 mm was the biggest among the separators investigated in this study, resulting that the dry up of PEM and catalyst layer was lower compared to the thinner separator thickness. It was also clarified the effects of separator thickness of profile gases, e.g., O2, H2O, and current density profile became larger under the higher temperature and the lower RH conditions.