A three-dimensional agglomerate model of an anion exchange membrane fuel cell has been developed and used to perform a parametric analysis of the effects of inlet relative humidity, ionomer water uptake, platinum loading, carbon content and ionomer volume fraction on the overall fuel cell performance. Improved cell performance has been obtained when the anode relative humidity was higher compared to the cathode resulting in a significant amount of water back diffusion, as well as higher oxygen partial pressure at the cathode enhancing the oxygen mass transport. Increasing the membrane water content positively affects the overall performance of the fuel cell because of the improvement of ionic conductivity. An increase in platinum loading has been found to have a positive impact on the fuel cell performance. Carbon loading influences the thickness of the catalyst layer, directly affecting concentration and Ohmic losses in the catalyst layer. An increase in the ionomer volume fraction enhances the transportation of ions and also the diffusion of membrane water through the membrane. A decrease in the volume fraction of ionomer in the catalyst layer leads to a reduction in the membrane water content and ion diffusion rate, thus deteriorating the overall performance of the fuel cell.