A mathematical model was developed to study the cathode catalyst layer (CL) performance of a proton exchange membrane fuel cell (PEMFC). A number of CL parameters affecting its performance are implemented into the CL agglomerate model. These parameters are: saturation and eight structural parameters, i.e., ionomer film thickness covering the agglomerate, agglomerate radius, platinum and carbon loading, membrane content, gas diffusion layer penetration content and CL thickness. An artificial neural network (ANN) approach along with statistical methods was used for modeling, prediction, and analysis of the CL performance, which is determined by activation over-potential. The ANN was constructed to develop a relationship between the named (input) parameters and activation overpotential. An statistical analysis, namely, analysis of means (ANOM) was performed on the data obtained by the trained ANN and resulted in the main effect of each input parameter, sensitivity factors of structural parameters and their mutual combination.