The present study seeks to investigate the impact of surface irregularities and cracks at the catalyst layer (CL) and microporous layer (MPL) interface on the mass and electronic transport of polymer electrolyte fuel cells (PEFCs). Two different CLs were compared, i.e. one with negligible cracking and the other with high cracking (≃6% contact surface area reduction), under a combination of various operating conditions, including high/low relative humidity, and the presence of nitrogen/helium inert gases in the cathode inlet stream. A limiting current density analysis indicated that the cracked CL demonstrated a small increase (0.5%) in the Fickian diffusion of the reactants across the cathode electrode compared to the negligible-cracked CL case. Furthermore, the results from a relative humidity analysis showed that the protonic resistance in the CL might dominate the moderate current density region (≃0.2 A/cm2<current density<0.45 A/cm2). Finally, comparison of the cell performance for cracked and negligible-cracked CL cases suggests that the cracks may act as water pooling sites, which in turn, may enhance the performance in the high current density region (current density>0.45 A/cm2) due to the decreased water surface coverage and/or enhanced water removal.