Numerous researchers use numerical simulations to precisely recognize the processes before mass-production to provide a basic model for optimizing the fuel cell. In this study, we presented brand-new designs for cylindrical PEMFCs in the Three-Dimensional form. We used the Finite Volume Method to simulate the fuel cell processes and established a genuine correspondence between our simulation results and valid outcomes. We introduced innovative designs to increase the performance of cylindrical polymer fuel cells. Then, we examined the effects of progressive developments in cross-section design, the fuel cell structure, the output current densities, and, eventually, the flooding phenomenon. The results revealed the optimum capacity of the cylindrical fuel cell compared with an elliptical cross-section. Due to more extensive transport zones and pressure drop effects, we need to find the optimum cell capacity to pass the reactive regions.