A comprehensive, three-dimensional analysis of a polymer electrolyte membrane (PEM) fuel cell has been developed to study the performance of this device under different operational conditions. This steady-state analysis is single-phase and non-isothermal. A commercial computational fluid dynamics (CFD) program provided a numerical platform for solving the conservation equations for species, energy, charge, mass and momentum. Different boundary conditions were added to a computational domain to simulate single channel PEM fuel cell. The electrochemistry involved in this model was added by a set of user-defined subroutines that feature: electrochemical reactions, electric and ionic charge and heat generation. The calculations were then solved by an iterative method following an adapted computational procedure. The results were validated with other computational models and experimental data. These show a noticeable non-uniform distribution of the current density across the catalyst layer (CL) at different operational conditions. The results emphasize on the differences of anodic and cathodic activation overpotentials, the oxygen transport limitations and the ohmic losses distributions of both proton and electric overpotentials.