A full three-dimensional, non-isothermal computational fluid dynamics model of a proton exchange membrane fuel cell (PEMFC) with both the gas distribution flow channels and the membrane electrode assembly (MEA) has been developed. A single set of conservation equations which are valid for the flow channels, gas-diffusion electrodes, catalyst layers, and the membrane region are developed and numerically solved using a finite volume based computational fluid dynamics technique. In this research some parameters such as Oxygen consumption and fuel cell performance according to the variation of porosity, thickness of gas diffusion layer, and the effect of the boundary conditions were investigated in more details. Numerical results shown that the higher values of gas diffusion layer porosity improve the mass transport within the cell, and this leads to reduce the mass transport loss. The gas diffusion layer thickness affects the fuel cell mass transport. A thinner gas diffusion layer increases the mass transport, and consequently the performance of the fuel cell. Furthermore, the study of boundary conditions effects showed that by insulating the bipolar surfaces, hydrogen and oxygen consumption at the anode and cathode sides increase; so that the fuel cell performance would be optimized. Finally the numerical results of proposed CFD model are compared with the available experimental data that represent good agreement.