Fuel cells (PEMFCs) are considered a clean alternative for the production of electricity. To improve their efficiency, it is necessary to understand the transport phenomena that determine their performance. This work analyzes the effective diffusion coefficients in the gas diffusion and catalyst layers (GDL and CL, respectively) based on theories such as effective medium approximation and percolation theory of a 3D multiphase nonisothermal model of a single channel PEMFC. We calculate polarization curves with different effective diffusion models and tortuosity factors m, n using OpenFOAM. The best model that approaches to experimental data is the Tomadakis-Sotirchos model with n = 4.0. The exponent m that represents the tortuosity due to the geometry has a high impact on the polarization curve construction compared to the exponent n. High values of diffusibility do not mean high values of current densities showing that there are other phenomena involved, such as water flooding.