Proton exchange membrane (PEM) fuel cells with a great potential for application in vehicle propulsion systems will have a promising future. However, to overcome the exiting challenges against their wider commercialization further fundamental research is inevitable. The effects of gas diffusion layer (GDL) compression on the performance of a PEM fuel cell is not well-recognized; especially, via pore-scale simulation technique capturing the fibrous microstructure of the GDL. In the current investigation, a stochastic microstructure reconstruction method is proposed which can capture GDL microstructure changes by compression. Afterwards, lattice Boltzmann pore-scale simulation technique is adopted to simulate the reactive gas flow through 10 different cathode electrodes with dissimilar carbon paper GDLs produced from five different compression levels and two different carbon fiber diameters. The distributions of oxygen mole fraction, water vapor mole fraction and current density for the simulated cases are presented and analyzed. The results of simulations demonstrate that when the fiber diameter is 9 mm adding compression leads to lower average current density while when the fiber diameter is 7 mm the compression effect is not monotonic. (C) 2017 Elsevier B.V. All rights reserved.