Using COMSOL Multiphysics 3.5, 3D numerical models of different microfluidic fuel cells have been developed in this paper to determine the effect of different modifications which have been implemented in the microfluidic fuel cell since its advent. These modifications include the channel geometry aspect ratio and electrode configuration, the third flow between the anolyte and catholyte in the channel (i.e., multi-stream laminar flow), and multiple periodically placed inlets. To be consistent with the convention, the output power of the device is normalized by the electrode surface area; however, the power density calculations are also performed through normalization by the device volume. It is shown that the latter method is more realistic and providing more information from the design point of view since the ultimate goal in designing the microfluidic fuel cell is to fabricate a compact, yet powerful device. Finally, a novel design of the microfluidic fuel cell with a tapered channel is suggested and compared to the non-tapered geometry through the polarization curves. The steps which have been taken in COMSOL to obtain these polarization curves are clearly and thoroughly explained. The Butler–Volmer equation was implemented to incorporate for the electrochemical reactions at the electrodes. The “Conductive Media DC” module, in COMSOL, is used to model the electric fields within the fuel cell. The concentration distributions of the reactant species are obtained using the “Incompressible Navier–Stokes” and “Convection and Diffusion” modules. Solving these equations together predicts the current density for given cell voltage values. The results demonstrate the cell voltage losses due to activation, ohmic and concentration overpotentials. It is shown that for a fixed value of the cell voltage (say 0.45V), the fuel cell with multiple periodically placed inlets has the highest fuel utilization (i.e., 62.3%); while the “Simple square” geometry depicts 13.8% fuel utilization at this potential. Thus, the multiple-inlets design is particularly suitable for low-voltage applications which require high current. Also, the results of the tapered geometry proposed in this paper show that tapering the channel enhances the polarization curve comparing to the square cross-section geometry with extended electrodes. In essence, the fuel utilization of the “Extended square” geometry is increased from 15.4% to 57.6% by tapering the channel. This is due to the fact that the mixing region growth rate is restricted in the tapered geometry, and hence the electrodes on the top and bottom walls of the channel can be more extended toward the centre of the channel before the crossover occurs.