Abstract We report a three‐dimensional (3D), pore‐scale analysis of morphological and transport properties for a polymer electrolyte fuel cell (PEFC) catalyst layer. The 3D structure of the platinum/carbon/Nafion electrode was obtained using nano‐scale resolution X‐ray computed tomography (nano‐CT). The 3D nano‐CT data was analyzed according to several morphological characteristics, with particular focus on various effective pore diameters used in modeling gas diffusion in the Knudsen transition regime, which is prevalent in PEFC catalyst layers. The pore diameter metrics include those based on chord length distributions, inscribed spheres, and surface area. Those pore diameter statistics are evaluated against computational pore‐scale diffusion simulations with local gas diffusion coefficients determined from the local pore size according to the Bosanquet formulation. According to our comparison, simulations that use local pore diameters defined by inscribed spheres provide effective diffusion coefficients that are consistent with chord‐length based estimations for an effective Knudsen length scale. By evaluating transport rates in regions of varying porosity within the nano‐CT data, we identified a Bruggeman correction scaling factor for the effective diffusivity.