The purpose of this study is to understand the impact of the thickness of Nafion membrane, which is a typical polymer electrolyte membrane (PEM) in Polymer Electrolyte Membrane Fuel Cells (PEMFCs), and relative humidity of supply gas on the distributions of H2, O2, H2O concentration and current density on the interface between a Nafion membrane and anode catalyst layer or the interface between a Nafion membrane and cathode catalyst layer. The effect of the initial temperature of the cell (Tini) is also investigated by the numerical simulation using the 3D model by COMSOL Multiphysics. As a result, the current density decreases along with the gas flow through the gas channel irrespective of the Nafion membrane thickness and Tini, which can be explained by the concentration distribution of H2 and O2 consumed by electrochemical reaction. The molar concentration of H2O decreases when the thickness of Nafion membrane increases, irrespective of Tini and the relative humidity of the supply gas. The current density increases with the increase in relative humidity of the supply gas, irrespective of the Nafion membrane thickness and Tini. This study recommends that a thinner Nafion membrane with well-humidified supply gas would promote high power generation at the target temperature of 363 K and 373 K.