A full three-dimensional, single phase 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, water production, velocity distribution, ohmic losses, liquid water activity and fuel cell performance for straight (base case) and prominent gas diffusion layers were investigated in more detail. The numerical simulations reveal that prominent gas diffusion layer improves the transport of the reactant gases through the porous layers; it is due to increase of the mentioned fuel cell efficiency, and prominent gas diffusion layers yield appreciably higher current density. Finally the numerical results of proposed CFD model (base case) are compared with the available experimental data that represent good agreement.