Biofuel cells are devices that use biocatalysts ( enzymes or microbes) to convert biochemical energy directly into electrical energy. Microfluidic biofuel cells exploit the lack of active mixing at microscale dimensions to eliminate the use of proton exchange membranes that separate anolyte and catholyte streams. Simulation of this system, by solving the governing 3-D conservation equations ( flow, species transport), reveals that oxygen availability limits the performance of the cathode. An exponential decay in the availability of oxygen at the cathode is observed along the length of the microchannel, indicating that increasing the number of electrode pairs reduces the overall current density. This conclusion is consistent with experimental observations. Increasing electrolyte flow rates can reduce the mass transport limitations by decreasing the diffusion boundary-layer thickness, but disparity between the flow rates of the anolyte and catholyte can induce wastage of dissolved oxygen.