Abstract This paper combines the stochastic-model-based reconstruction of the gas diffusion layer (GDL) of polymer electrolyte fuel cells (PEFCs) and direct simulation to investigate the pore-level transport within GDLs. The carbon-paper-based GDL is modeled as a stack of thin sections with each section described by planar two-dimensional random line tessellations which are further dilated to three dimensions. The reconstruction is based on given GDL data provided by scanning electron microscopy (SEM) images. With the constructed GDL, we further introduce the direct simulation of the coupled transport processes inside the GDL. The simulation considers the gas flow and species transport in the void space, electronic current conduction in the solid, and heat transfer in both phases. Results indicate a remarkable distinction in tortuosities of gas diffusion passage and solid matrix across the GDL with the former ∼1.2 and the latter ∼13.8. This difference arises from the synthetic microstructure of GDL, i.e. the lateral alignment nature of the thin carbon fiber, allowing the solid-phase transport to occur mostly in lateral direction. Extensive discussion on the tortuosity is also presented. The numerical tool can be applied to investigate the impact of the GDL microstructure on pore-level transport and scrutinize the macroscopic approach vastly adopted in current fuel cell modeling.