The gas diffusion layer (GDL) in a proton exchange membrane (PEM) fuel cell has a porous structure with anisotropic and non-homogenous properties. The objective of this research is to develop a PEM fuel cell model where transport phenomena in the GDL are simulated based on GDL’s pore structure. The GDL pore structure was obtained by using a scanning electron microscope (SEM). GDL’s cross-section view instead of surface view was scanned under the SEM. The SEM image was then processed using an image processing tool to obtain a two-dimensional computational domain. This pore structure model was then coupled with an electrochemical model to predict the overall fuel cell performance. The transport phenomena in the GDL were simulated by solving the Navier-Stokes equation directly in the GDL pore structure. By comparing with the testing data, the fuel cell model predicted a reasonable fuel cell polarization curve. The pore structure model was further used to calculate the GDL permeability. The numerically predicted permeability was close to the value published in the literature. A future application of the current pore structure model is to predict GDL thermal and electric related properties.