Among the parameters to take into account in the design of a proton exchange membrane fuel cell (PEMFC), the energy conversion efficiency and material cost are very important. Understanding in deep the behavior and properties of functional layers at the microscale is helpful for improving the performance of the system and find alternative materials. The functional layers of the PEMFC, i.e., the gas diffusion layer (GDL) and catalyst layer, are typically porous materials. This characteristic allows the transport of fluids and charges, which is needed for the energy conversion process. Specifically, in the GDL, structural parameters such as porosity, tortuosity, and permeability should be optimized and predicted under certain conditions. These parameters have effects on the performance of PEMFCs, and they can be modified when the assembly compression is effected. In this paper, the porosity, gas-phase tortuosity, and through-plane permeability are calculated. These variables change when the digitally created GDL is under compression conditions. The compression effects on the variables are studied until the thickness is 66% of the initial value. Because of the feasibility to handle problems in the porous media, the fluid flow behavior is evaluated using the lattice Boltzmann method. Our results show that when the GDL is compressed, the porosity and through-plane permeability decrease, while the gas-phase tortuosity increases, i.e., increase the gas-phase transport resistance. Copyright (c) 2015 John Wiley & Sons, Ltd.