The goal of this study is to design a gas diffusion layer (GDL) for a polymer electrolyte membrane (PEM) fuel cell with a graduated permeability and thereby graduating the resistance to flow throughout the GDL. It has been shown that in using conventional materials, the GDL exhibits a higher resistance in the through-plane direction due to the orientation of the small carbon fibers that make up the carbon paper or carbon cloth. In this study, a GDL is designed for an unconventional PEM fuel cell stack where the reactant gases are supplied through the side of the GDL rather than through flow field channels machined into a bipolar plate. The effects of changing in-plane permeability, through-plane permeability, GDL thickness, and oxygen utilization on the expected current density distribution at the catalyst layer are studied. Three different thicknesses and three different utilizations are investigated. It has been found that a thinner GDL with a lower utilization yields a higher current density on the electrode. A quantitative metric to measure uniformity of reactant distribution and the ratio of the standard deviation of the current density to the average current density was introduced, and it was found that while the uniformity of the reactant distribution is independent of thickness of the GDL, it is inversely proportional to utilization.