Microfluidic fuel cells operate in the laminar flow regime, thus their fuel utilization is low. A trade-off exists between fuel utilization and output power density. To achieve high output power density and fuel utilization simultaneously, several parameters should be optimized. We have employed a multi-objective optimization method to optimize a simple Y-shaped microfluidic fuel cell with rectangular cross section channel. An electrochemical model for microfluidic fuel cell in MATLAB environment is developed and validated. By coupling this model with multi-objective optimization algorithm the multi-objective optimization problem is defined. Genetic algorithm is used to solve this multi-objective optimization problem. The Pareto set, represents a quantitative description of the trade-off between power density and fuel utilization. The results show that to make the most of the power density-fuel utilization trade-off behavior, fuel cell should be operated at current density no more than 0.9 mW/cm(2). Almost for all solutions in Pareto set, the values of channel width and fuel concentration are 0.5 mm and 12 mol/m(3), respectively.