Modeling and simulation for heat and mass transport in micro channel are being used extensively in researches and industrial applications to gain better understanding of the fundamental processes and to optimize fuel cell designs before building a prototype. In this study, a full numerical, three-dimensional, single phase computational fluid dynamics (CFD) 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 are developed and numerically solved using a finite volume based CFD technique. The present simulated single straight channel PEMFC model, accounts the major transport phenomena and the performance. Additionally, the effect of inversing the flow direction at cathode side (counter flow PEMFC) has been investigated on the fuel cell performance and species distribution. The results showed that, in the with the counter flow channels, the output current density has been decreased and also the kind of species distributions has been influenced by this phenomenon. It is very important to model the back diffusion and electro-osmotic mass flux accurately since the two fluxes was closely correlated each other and greatly influenced for determination of ionic conductivity of the membrane which directly affects the performance of fuel cell. Finally, the numerical results validated by available experimental data.