The catalyst layer (CL) of the polymer electrolyte membrane (PEM) fuel cell must be modeled accurately in order to resolve the effects of complex interactions between charge and mass transport on the fuel cell's electrochemical reactions. In previous work, we developed an agglomerate model [1] which correctly accounts for variations in the agglomerate surface area as the CL constituents are varied to provide a better estimate of diffusion losses. Here, this improved agglomerate model is employed to investigate a PEM fuel cell catalyst layer with a functionally-graded composition. We present results for varying catalyst and ionomer loadings in both the through-thickness and in-plane directions. In agreement with experimental observations, we find that a higher catalyst and/or ionomer loading at the membrane/CL interface improves performance especially in the ohmic loss regime. Similarly, improved performance is observed for higher catalyst and/or ionomer loadings under the channel in the mass transport loss regime. In addition, we investigated bidirectionally graded CLs for the first time. It is observed that higher performance can be obtained with bidirectionally graded CLs in both ohmic and mass transport loss regimes. (C) 2014 Elsevier B.V. All rights reserved.