This work represents a mathematical model for a typical PEM fuel cell operated with non-precious carbon-based materials as ORR catalysts. The PEM fuel cell is operated at a practical single-cell condition, thus the reactant transport issues are taken into account. The model includes majority of critical significant physical and electrochemical processes during operation. The catalyst layer is assumed to be constructed by carbon agglomerates, in which the active sites for ORR are uniformly embedded and distributed. The catalyst loading, catalyst to ionomer mass ratio and catalyst layer porosity are numerically studied. Results reveal the significance of reactant transport within the carbon agglomerates, indicating the vital important role of primary pores for reactant transport and cell performance. It is found that the initial increase in catalyst loading and porosity improves the cell performance. However, their further increment results in limited improvement due to the elevated mass transport resistance in a thickened catalyst layer. Higher catalyst to ionomer ratio decreases the cell performance at low and medium current densities. The catalyst effectiveness can be improved with low catalyst loading, high catalyst layer porosity and catalyst to ionomer mass ratio. (C) 2018 Elsevier Ltd. All rights reserved.