Performance of polymer electrolyte membrane fuel cells (PEMFC) at high current densities is limited to transport reactants and products. Furthermore, large amounts of water are generated and may be condensed due to the low temperature of the PEMFC. Development of a two-phase flow model is necessary in order to predict water flooding and its effects on the PEMFC performance. In this paper, a multiphase mixture model (M2) is used, accurately, to model two-phase transport in porous media of a PEMFC. The cathode side, which includes channel, gas diffusion layer (GDL), microporous layer (MPL), and catalyst layer (CL), is considered as the computational domain. A multidomain approach has been used and transport equations are solved in each domain independently with appropriate boundary conditions between GDL and MPL. Distributions of species concentration, temperature, and velocity field are obtained, and the effects of MPL on species distribution and fuel cell performance are investigated. MPL causes a saturation jump and a discontinuity in oxygen concentration at the GDL/MPL interface. The effect of MPL thickness on fuel cell performance is also studied. The results revealed that the MPL can highly increase the maximum power of a PEMFC.