In this study, a three-dimensional (3D) agglomerate model of an anion exchange membrane (AEM) fuel cell is proposed in order to analyze the influence of the composition of the catalyst layers (CLs) on overall fuel cell performance. Here, a detailed comparison between the agglomerate and a macrohomogeneous model is provided, elucidating the effects of the CL composition on the overall performance and the individual losses, the effects of operating temperature and inlet relative humidity on the cell performance, and the CL utilization by the effectiveness factor. The results show that the macrohomogeneous model overestimates the cell performance compared to the agglomerate model due to the resistances associated with the species and ionic transports in the CLs. Consequently, the hydration is negatively affected, resulting in a higher Ohmic resistance. The activation overpotential is overpredicted by the macrohomogeneous model, as the agglomerate model relates the transportation resistances within the domain with the CL composition. Despite the higher utilization in the anode CL, the cathode CL utilization shows a significant drop near the membrane–CL interface due to a high current density and a low oxygen concentration. Additionally, the influences of operating temperature and relative humidity at the flow channel inlet have been analyzed. Similar to the macrohomogeneous model, the overall cell performance of the agglomerate model is enhanced with increasing operating temperature due to the better electrochemical kinetics. However, as the relative humidity at the inlet is reduced, the overall performance of the cell deteriorates due to the poor hydration of the membrane.

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