The configuration of the flow channel on a bipolar plate of a proton exchange membrane fuel cell(PEMFC) for efficient reactant supply has great influence on the performance of the fuel cell. Recent demand for higher energy density fuel cells requires an increase in current density at mid voltage range and a decrease in concentration overvoltage at high current density. Therefore, an interdigitated flow channel where mass transfer rate by convection through a gas diffusion layer is greater than the mass transfer by a diffusion mechanism through a gas diffusion layer was recently proposed. This study attempts to analyze the i-V performance, mass transfer and pressure drop in interdigitated flow channels by developing a fully three dimensional simulation model for PEMFC that can deal with anode and cathode flow together. The results indicate that the trade off between performance and pressure loss should be considered for efficient design of flow channels. Although the performance of the fuel cell with interdigitated flow is better than that with conventional flow channels due to a strong mass transfer rate by convection across a gas diffusion layer, there is also an increase in friction due to the strong convection through the porous diffusion layer accompanied by a larger pressure drop along the flow channel. It was evident that the proper selection of the ratio of channel and rib width under counter flow conditions in the fuel cell with interdigitated flow are necessary to optimize the interdigitated flow field design.