The performance of a polymer electrolyte fuel cell can be enhanced by improving the proton conductivity of the catalyst layer, where the oxygen reduction reaction generates electrochemical power. Protons are conducted through the ionomer coatings on catalyst-supporting carbon particles, which form porous structures that facilitate oxygen diffusion during the reaction within the catalyst layer. Therefore, while a higher ionomer content in the catalyst layer is favorable, the proton conductivity is additionally governed by the type of carbon support. As the influence of the ionomer distribution is not fully understood, we introduce a novel proton conductivity model for use in simulating catalyst layers with various amounts of ionomers and different carbon types. This proton conductivity model considers that several ionomers occur as thin films with drastically suppressed proton conductivities. Although evaluating the thin-film ionomer fraction is challenging, proton-conducting ion clusters in thick-film ionomers have been detected by characterizing the catalyst layers via small-angle neutron scattering. Our model reveals that reducing the fraction of the thin-film ionomer or avoiding factors that suppress its proton conduction improves the performance of the catalyst layer.