An important obstacle to overcome in the advancement of microbial fuel cell (MFC) technology is improving the effectiveness of the micro-channel components in a MFC system. Through the use of a commercial computational fluid dynamics (CFD) simulator, this study analyzed four micro-channel designs and collected data pertaining to velocity and pressure distribution, and pressure drop. Factors considered in the study included inlet aspect ratios and variable inlet Reynolds numbers. Simulation outputs and experimental testing all indicated that an innovative biometric configuration yielded the best combination of all the parameters, producing the most consistent mass flow rate and the second-lowest pressure trend. Other designs were deemed less effective due to detrimental characteristics such as inconsistent flow patterns or undesirable pressure levels. These findings would be useful to the further design of microbial fuel cell system.