In this study, 6 different novel flow channels of the "proton exchange membrane" (PEM) type fuel cells were designed and modeled, while evaluations were conducted on three-dimensional channels of various designs using COMSOL Multiphysics simulation software. Proposed fuel cell designs and flow channel geometries were compared to existing exergetically-efficient fuel cell designs in terms of total exergy efficiency in a 3D manner as a novel tool for fuel cell investigations. Exergy efficiency analyses were conducted on the membrane surfaces of the proposed designs in addition to the anode and cathode side exergy analyses, and exergetic efficiencies of the alternatives. It is found that Design 6 is the best flow channel design with relatively high values and homogeny in exergy efficiency. The multi-inlet/outlet style while sustaining the reaction long enough for the reactant depletion leads to high-efficiency levels as seen from the results with average efficiency of 24%.