In the present work, the anisotropic effective thermal conductivity of the gas diffusion layer (GDL) of a polymer electrolyte membrane (PEM) fuel cell is determined using a thermal lattice Boltzmann model. Using saturation patterns obtained from three-dimensional pore network modeling simulations with invasion percolation, the thermal conductivity of the GDL containing liquid water is determined. For a GDL modeling domain with a total saturation of 24.4% (flooded inlet condition), increases of 20.8% and 5.4% are noted for the through-plane and in-plane thermal conductivities, respectively. As the GDL plays an important role in thermal and water management within a PEM fuel cell, the simulated thermal conductivities determined in this work can provide insight into the effect of the GDL on the thermal management required for improved PEM fuel cell performance. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.014212jes] All rights reserved.