Design optimization of current collectors has been performed to reduce the significant ohmic resistance observed in microfluidic fuel cell (MFC) with flow-through porous electrodes. A three-dimensional computational model is developed to investigate the electron transport characteristics in the porous electrodes, where lateral electron transport is found to encounter high resistance. Influences of different current collector design parameters on the transport resistances are examined and analyzed. The modeling results indicate that current collector position is the most influential factor due to the non-uniform flow rate distribution. Optimal current collector position is located at the high flow rate region instead of the conventional exposed end of the porous electrode. Experimental studies are performed to support the modeling analysis. The experimental results demonstrate that the optimized current collector position can boost the maximum power density by 61%. This study highlights the significance of the current collector design in achieving high performance MFC with flow-through porous electrodes. Based on the results, some general rules have been set for the current collector designs in this energy system, which can provide useful guidance for the future development of MFC.