This study covers the three dimensional analysis of a single-cell proton exchange membrane fuel cell (PEMFC) by using ANSYS-FLUENT program for two different dimensioned of Membrane Electrode Assembly (MEA). Two prepared MEA with different thickness dimensions were implemented to PEM fuel cell and analyzed numerically by using ANSYS-FLUENT. In the first MEA, the thicknesses of gas diffusion layer, catalyst layer and membrane were selected as 0.400 mm, 0.005 mm and 0.035 mm, respectively. For the second MEA these thicknesses were selected for gas diffusion layer as 0.300 mm, for catalyst layer as 0.050 mm. and for membrane as 0.125 mm and numerically analyzed by using dimensional properties of second MEA. For these two different MEAs which have different thicknesses, were used in PEM fuel cell model, polarization curves obtained and compared. As a result of solutions were obtained for MEA-1 having a catalyst layer with a thin thickness, the region corresponding to concentration losses occurs in the polarization curve can be seen. The current density values obtained from the solution of the prepared fuel cell models with MEA-1 were significantly better than the case derived with MEA-2. for PEM fuel cell model, the effect of operating pressure on the current density was analyzed by using these two different thicknesses MEAs (MEA-1 and MEA-2). Operating pressures were determined as 150 kPa, 200 kPa, 300 kPa and 400 kPa. For each operating pressure value determined polarization curves are presented in graphs for both MEA. For the solution of the problem, basic principles such as conservation of mass, momentum, energy, species, and phase potential are considered. In ANSYS FLUENT PEMFC module, electrochemical equations depending on hydrogen oxidation and oxygen reduction rates are solved. The results of hydrogen and oxygen mass fraction distributions are presented along the gas flow main direction. Furthermore, hydrogen mass fraction distributions are analyzed at the cross sections (inlet, mid-way, outlet) perpendicular to the main flow direction.