Due to low oxygen solubility in the electrolyte, creating a depletion layer on the cathode surface is an important factor in reducing the performance of the microfluidic fuel cell. In this paper, for improving the mass transfer to the surface of the cathode in the Y-shaped microfluidic fuel cell with a flow over structure, a novel cathode structure is presented. Here, the conventional cathode is divided into smaller parts, and these parts are placed in the path of the oxidant flow. We consider the microfluidic fuel cell with liquid phase fuel and oxidant streams operate at room temperature T = 298 K. Results show that due to the appropriate mass transfer rate to the surface of the proposed cathode, the possibility of the formation of the depletion area on the cathode surface is reduced. In the proposed structure of the cathode, both the initial parts of the cathode and the end parts of the cathode play a role in generating electric current, and as a result, the output current density of the cell increases. The results show that the electric current density and the peak power density of the proposed cell are significantly higher than conventional cells at both low and high reactant flow rates.