The role of the cathode microporous layer (MPL) of the gas diffusion layer (GDL) in a polymer electrolyte exchange membrane fuel cell (PEMFC) was investigated by comparing the performance of several cells containing different MPLs. The capillary pressure and permeability of the GDL play an important role in the transport of water generated in the PEMFC. MPLs were prepared with different hydrophobic agent contents to impart different water capillary pressures and hydrophobic properties. Under dry inlet air conditions, the cell without an MPL exhibited better performance than those with MPLs. In contrast, under wet inlet air conditions, the performance of the cell without an MPL decreased significantly at a relatively low current density, and the cell with the highest capillary pressure MPL exhibited the best performance. These experimental data were evaluated according to the water vapor activity of the cathode, which was modified with the capillary pressure of the MPL. As a result, the modified activity was determined to be a key factor to explain the occurrence of cathode flooding. Liquid water saturation in the diffusion media (GDL, MPL) and the cathode catalyst layer (CCL) are determined by the balance of capillary pressures of the pores of each layer. Increase of the diffusion resistance of oxygen in the CCL is significant, while that in the diffusion media is moderate, which indicates that the CCL is susceptible to flooding.