For the polymer electrolyte fuel cell (PEFC), the separator thickness plays an important role to determine the weight, the volume and the costs of the PEFC. In addition, thermal management, i.e. temperature distribution is also important for the PEFC system to obtain higher performance. However, there were few reports investigating the relationship between the temperature distribution and the power generation performance such as current density distribution of PEFC operated at higher temperature (HT-PEFC). The aim of this study is to clarify the impact of separator thickness on the relationship between the temperature distribution and the current density distribution of HT-PEFC. This study has also investigated the impact of separator thickness on the relationship between the temperature distribution and the gases such as H2, O2 and the current density distribution of HT-PEFC numerically using CFD software COMSOL Multiphysics. The separator thicknesses of 2.0 mm, 1.5 mm and 1.0 mm were studied. In the study, the operation temperature and the relative humidity (RH) of supply gas were also changed. As a result, it was revealed that the optimum separator thickness was 2.0 mm to obtain higher power generation of HT-PEFC. Since the heat capacity in the case of the separator thickness of 2.0 mm was the largest among the separators investigated in this study, the dehydration of PEM and catalyst layer was smaller compared with the thinner separator thicknesses. It was also revealed that the impacts of separator thickness on distribution of gases, e.g. O2, H2O, and current density distribution became larger under higher temperature and lower RH conditions. This study also concluded that the tendency of temperature distribution matched those of O2, H2O and current density distributions.