In this work, the effect of fibre surface morphology on the effective thermal conductivity of the gas diffusion layer of a polymer electrolyte membrane fuel cell is presented. Atomic force microscopy was used to measure the fibre surface roughness and asperity height distributions for various fibres for Toray carbon paper. Hertzian contact mechanics was used to determine individual micro-contact areas and thermal resistances, and results were compared with the smooth cylinder approximation. The effective thermal contact resistance between rough fibres was determined using resistance network theory. The thermal contact resistance and total contact area were determined for various angles of fibre orientation and contact forces; results are presented as empirical formulations. It was found that the effective thermal contact resistance is significantly affected by fibre roughness features when compared to the smooth fibre case, which is often used in the literature. The analysis conducted provides an alternative to computationally expensive surface feature analyses by providing a tool which can be used to implement the nano-scale features of gas diffusion layer fibres into existing effective thermal conductivity models.