Computation of Proton Exchange Membrane (PEM) fuel cell's cathode Catalyst Layer (CL) is performed using agglomerate models in this paper, and the results are compared with homogenous one. Following our earlier homogenous model for cathode CL (see Khajeh-Hosseini et al., 2010), the focus of the present study is on agglomerate model. In this study, the derivation of agglomerate model is performed in such a way that in the simplified case when agglomerate sizes shrink to zero, the homogeneous model condition is retrieved. Validations versus two sets of experimental data are performed. For example, in one of the validation cases, Case (II), it is observed that in I-tot = 3000 [A m(-2)] the homogeneous model overestimates the performance by 80%. But the agglomerate model agrees well with the validating test cases. A set of parametric studies are performed using the agglomerate model, in which the influences of some CL structural- and cell operating-parameters are studied. A sensitivity study on the cell performance is performed to rank the influence of the parameters, with rank 1 for the most influential parameter. It is observed the agglomerate sizes possess rank 1. These results give useful guidelines for manufactures of PEMFC catalyst layers. Copyright (c) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.