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The performance of proton exchange membrane fuel cell (PEMFC) under different membrane geometries is investigated using a three-dimensional mathematical model. The proton exchange membrane fuel cell is mainly composed of bipolar plates, a gas diffusion layer, a micro porous layer, a catalyst layer, and a membrane. The numerical model is simulated in the comsol multiphysics to study the effects of different membrane geometries on the performance of the proton exchange membrane fuel cell. The results show that the performance of the proton exchange membrane fuel cell improves as the membrane's thickness is scaled down towards being nanoscale. The model was compared with experimental trends and there is a good agreement between experimental data trends and the proposed model.