Abstract The transport of electrons through the gas diffusion layer (GDL) of polymer electrolyte membrane (PEM) fuel cells has a significant impact on the optimal design and operation of PEM fuel cells and is directly affected by the anisotropic nature of the carbon paper material. In this study, a three-dimensional reconstruction of the GDL is used to numerically estimate the directional dependent effective electrical conductivity of the layer for various porosity values. The distribution of the fibers in the through-plane direction results in high electrical resistivity; hence, decreasing the overall effective electrical conductivity in this direction. This finding is in agreement with measured experimental data. Further, using the numerical results of this study, two mathematical expressions were proposed for the calculation of the effective electrical conductivity of the carbon paper GDL. Finally, the tortuosity factor was evaluated as 1.7 and 3.4 in the in- and through-plane directions, respectively.