Hydrophobicity and porosity of the gas diffusion layer (GDL) are key parameters in optimizing the design of proton-exchange membrane (PEM) fuel cells. Their effects on cell performance are analyzed using the ANSYS PEM fuel cell module, with simulation results compared with available experimental data. The simulations indicate that increasing the contact angle of the GDL up to 150 degrees enhances liquid water removal and cell performance, but there is a little gain in exceeding this value. Experimental tests of a cell with a poly(tetrafluoroethylene) (PTFE)-coated GDL and high contact angle and a cell with an uncoated GDL confirmed this finding from the simulation. The modeling further indicated that increasing the porosity of the GDL from 0.4 to 0.6 boosted power output by enhancing gas transport and liquid water removal. Within the ANSYS module, a 20% variation in the exponents of pores blockage and reducing active sites did not affect cell performance significantly.