The heat generation inside polymer electrolyte membrane (PEM) fuel cells affects fuel cell performance significantly. A numerical model for three-dimensional single fuel cell is developed by including the energy equation and the phase change aspects. A control volume approach is used and source terms for species transport equations, heat generation, and phase change model are introduced to incorporate the coupled flow physics in commercial flow solvers. Details of local current density distribution and temperature profiles are obtained and predictions from this model are compared with previous conclusions. The results reveal that the water evaporation and condensation generated by temperature change in fuel cell control humidity of the membrane and vary the local current density value. Further, the temperature distributions are dependent on the amount of heat generation created by electrical losses and water phase change. The predictions also present that the performance of the fuel cell relies not only on the inlet humidity condition but also on the temperature change inside the fuel cell.