The influence of microporous layer (MPL) design parameters for gas diffusion layers (GDLs) on the performance of polymer electrolyte fuel cells (PEFCs) was clarified. The appropriate MPL design parameters vary depending on the humidification conditions of the supplied gases. Under high humidification, a decrease in the MPL pore diameter is effective for the prevention of flooding and the enhancement of the PEFC performance. However, when the pore diameter becomes too small, the PEFC performance tends to decrease. Reducing the MPL thickness penetrated into the substrate improves in-plane permeability, and enhances the ability of the MPL to avoid flooding. Under low humidification, a decrease in the MPL pore diameter is effective to prevent drying-out of the MEA. Increasing the MPL thickness is also effective for maintaining the humidity of the MEA. However, when the MPL thickness becomes too large, oxygen transport to the electrode through the MPL is reduced, lowering the PEFC performance.