In present paper it is tried to concentrate to the configurations of gas channels and gas diffusion layers influences on the performance of polymer electrolyte membrane fuel cell. At first, increasing the number of channels is considered and observed such that the best results are gained with the case of three channels. Afterward, effect of prominent GDLs is studied. The prominences size is one of the main parameters which affect the performance. For this purpose, radius (R) of prominences is grown gradually. The optimal performance is obtained in the case of R = 0.45. In addition, the inlet velocity of gas flow is surveyed. The results indicate that when the inlet velocity of gases is set about 0.2 m s −1 , the species diffusion is optimized. Also, the height of channels is investigated to find out the optimal channel height. It is found that the highest performance is achieved in channel height about h = 1 mm and R = 0.45 mm.