Catalyst layer is one of the important components of PEM fuel cell that its modeling and optimization can have a significant effect on the performance and the price of fuel cell. Despite successes were obtained to improve the fuel cell performance but still the slow reaction of oxygen in the cathode catalyst layer and mass transfer limitations are the main factors that reduce the efficiency and the performance of PEM fuel cell. The aim of this paper is modeling the cathode catalyst layer with homogeneous and agglomerate models and comparison with together. The governing equations are including oxygen diffusion equation, electrochemical reaction rate equation, transport equations of protons and electrons and auxiliary equations that solved by Matlab software and validated with experimental and numerical data available in the literature. The results show that at constant porosity, with increasing the agglomerate radius and thickness of ionomer film around agglomerate, the activation loss is increased and the concentration is reduced therefore the fuel cell performance is reduced. By more decreasing the radius of agglomerate, the fuel cell performance curve base on the agglomerate model approach to the performance curve base on the homogenous model.