Membraneless microfluidic fuel cells are miniaturized and integratable power sources as compared with conventional fuel cells based on membrane electrode assembly. To elucidate the interaction of two-phase flow, mass transport and electrochemical reactions, a two-dimensional two-phase model is developed for the microfluidic fuel cell with a flow-through porous anode. The two-phase flow in the anode and the microchannel is formulated by the two-fluid model and mixture multiphase flow theory, respectively. The modelling results suggest that the retention of gas phase in the anode catalyst layer and microchannel can reduce the effective active area and impede the proton conduction to limit the cell performance. However, the commonly used single-phase assumption fails to capture these effects, resulting in overestimated performance. The fuel crossover shows an opposite trend as compared with that predicted by the previous single-phase model, and is found to correlate with the two-phase flow in the microchannel. The flow rates of fuel and electrolyte on the fuel transport and gasphase removal are also discussed. The present work highlights the significance of two-phase effects in the modelling of microfluidic fuel cells, and provides insights into the two-phase flow and mass transfer for future development and operation.