The safe and efficient working of fuel cells depends on the thermal management of the heat generated during the electrochemical process. The aim of the article is to study the thermal transport phenomenon in polyether ether ketone (PEEK) using molecular dynamics (MD) based simulations. MD simulations were performed in conjunction with hybrid force fields. The effect of the degree of polymerization, crystallinity, sulfonation and the concentration of water on the thermal conductivity of PEEK was explored in this article. The Müller-Plathe algorithm was used to predict the thermal transport phenomenon in PEEK and S-PEEK. It was predicted from the simulations that the degree of polymerization and crystallinity significantly affect the thermal conductivity of PEEK, whereas the attachment of a sulfur group mitigates the thermal transport in S-PEEK. Addition of water molecules to PEEK and S-PEEK configurations leads to an enhancement in the thermal conductivity, and the effect is more prominent in S-PEEK configurations. The efficient thermal transport in the polymeric membranes of fuel cells helps in improving the working and lifecycle of the membranes.