The gas diffusion layer is an anisotropic porous medium, which provides pathways for the reactant gases and produced water, conducts the electrical current, removes the generated heat, and provides mechanical support. However, the gas diffusion layer is mostly considered as isotropic in numerical simulations. In the present study, a three-dimensional, two-phase flow, and non-isothermal agglomerate model with consideration of anisotropic permeability, mass diffusivity, thermal conductivity, and electrical conductivity was developed and employed to investigate effects of anisotropic properties on the transport phenomena in a proton exchange membrane fuel cell. The temperature of the anisotropic case is less than that of the isotropic case, and the temperature difference increases with increasing current density. Furthermore, the distributions of the oxygen mass fraction, liquid water saturation, water content, and local current density for both cases are also compared and discussed in detail. The cell performance is over-predicted by the isotropic model, and the current density of the isotropic case is greater than that of the anisotropic case by approximately 10% at an operating cell voltage of 0.3V. Both the local transport characteristics and overall cell performance are different for the isotropic and anisotropic cases. Accordingly, it is concluded that the anisotropic properties of the gas diffusion layer must be taken into account in the mathematical model. Copyright (c) 2017 John Wiley & Sons, Ltd.