To achieve an optimal perception of cardinal processes and prior to prototype fabrication to fuel cell optimization, modeling is extensively used in industrial researches and applications to transfer mass and heat into small-sized channels. In the current study, Computational Fluid Dynamics is presented to cylindrical polymer fuel cell with circular and elliptical cross-section. Concurrently, the design of fractured electrode-membrane assembly is introduced. The simulations explicitly demonstrate comparing to Base case production, the fractured case of the Electrode Membrane Assembly produces more current. Likewise, a new design for cylindrical polymer fuel cell is illustrated. In the cylindrical design, both the effect of gradual geometric changes on the performance including radius changes and the transformation of cross-section from circle to ellipse has been investigated and compared to Base case. The obtained results displays the cylindrical fuel cell’s better performance compared to Base case. Accordingly, establishing wider passage, in same volume for reactive gases toward reaction areas, results in sharp increase in the performance. Finally, validating simulation with valid laboratory results, proper correspondence is achieved.