Heat transfer through the gas diffusion layer (GDL) is a key process in the design and operation of a PEM fuel cell. The analysis of this process requires determination of the effective thermal conductivity. This transport property differs significantly in the through-plane and in-plane directions due to the anisotropic micro-structure of the GDL. In the present study, a novel test bed that allows the separation of in-plane effective thermal conductivity and thermal contact resistance in GDLs is described. Measurements are performed using Toray carbon paper TGP-H-120 samples for a range of PTFE content at a mean temperature of 65–70°C. The measurements are complemented by a compact analytical model that achieves good agreement with the experimental data. The in-plane effective thermal conductivity is found to be about 12 times higher than the through-plane conductivity and remains approximately constant, k ≈ 17.5 W/mK, over a wide range of PTFE content.