In this study, parametric study on the cathode catalyst layer in a Proton Exchange Membrane (PEM) fuel cell was conducted. Steady-state, two dimensional (2D) and non-isothermal conditions were proposed as critical hypotheses of work in essence. Multicomponent mass diffusion along with convection mechanism in a single cell, conduction changes of proton and electron with experimental data and Knudsen diffusion which has a crucial impact on the simulation task in nanoscale, were considered in our study. Moreover, carbon nanotube (CNT), platinum (Pt) and Nafion loading effects as well as the porosity characteristics in a single-phase flow at different catalyst layer (CL) thicknesses were thoroughly investigated. The results presented herein, revealed that the amount of Pt and CNT has more profound effect than catalyst porosity. Based on the results derived, the model presented could be a promising mean to develop and construct a nanostructured catalyst layer. Meanwhile, our modified agglomerate model predicts the performance of fuel cell systems in different experimental conditions. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published. by Elsevier Ltd. All rights reserved.