Lattice Boltzmann method is an effective tool for depicting all transport phenomena governed by advection-diffusion-reaction mechanisms. In the present study, five different cathode catalyst layers of PEM fuel cells with dissimilar morphologies are stochastically reconstructed. The agglomerates of carbon black particles are considered as ellipsoids which can have different level of stretching. The reactive air flow through the reconstructed catalyst layers is simulated by 3D lattice Boltzmann agglomerate modeling for the first time. Species distributions in the pore region, electrical potential distribution in the electrolyte film, and current density distribution at the interface of catalyst layer and membrane are depicted and analyzed. The results of this study show that oxygen and water vapor mole fraction variation is unsmooth and disturbed; and by increasing of ellipsoid stretching, this unsmooth and disturbed manner becomes more severe. Besides, the water content of the electrolyte film remains at its initial value mostly at the top of upper agglomerates while higher water content is observed where the agglomerates are closer to each other. Moreover, the catalyst layer in which ellipsoidal agglomerates have the highest level of stretching provides the maximum average current density. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.