In the present study we report on numerical investigations into the effects of compression on the performance of a unit cell. The focus of this study is how the transport properties of the gas diffusion layer (GDL) material, specifically porosity and permeability, affect numerical predictions of cell performance. Experimental data of porosity and permeability of uncompressed and compressed GDLs were obtained using a porometer, and used in numerical simulations. A 3D model with two parallel channels and an membrane electrode assembly (MEA) is constructed for the calculations. Three different configurations of transport properties were tested, i.e. uniform uncompressed GDL properties, uniform compressed GDL properties, and non-homogeneous GDL properties. It is found that the non-homogeneous case shows noticeable differences in predicted cell performance. For the non-homogenous case, simulations with a pressure difference between two cathode channels were carried out to gain insight into the effect of cross-channel flow on the overall prediction of cell performance. We found that the cross-channel flow changes local current density distribution primarily on the high-pressure channel. The present study demonstrates the importance of the proper use of transport properties for the compressed portion of the GDL.