Diffusion boundary layer on the electrode surface of microfluidic fuel cells limits the mass transfer to the catalyst layer. Thus, investigation of the transient response of microfluidic fuel cell associated with the change in operating condition is not a trivial work. In this paper, transient characteristics of a microfluidic fuel cell upon changes in voltage load is investigated by applying a transient three-dimensional, two-phase and non-isothermal numerical model. Proposed model is developed with COMSOL multi-physics and governing equations are formulated based on the conservation laws for mass, momentum, species and electrical potentials. This model evaluates the effect of a dominant dynamic aspect of MFFC operation (mass transfer effect), accounts for transient convective and diffusive transport, and allows prediction of species concentration. Simulation results show that during step voltage change, the transient current lags behind voltage due to the time constant of reactant species transport. Also, simulation results show that the over/under shot of the current density occurs during the step change in the fuel cell voltage. The limited mass transport in the diffusion boundary layer causes a time delay between the voltage step change and the change of reactant distribution on the electrode surface. During the step voltage decrease/increase, the initial higher/lower reactant concentration on the electrode surface causes the over/under-shoot of current density. Simulation results show that the properties of the current over/undershoot can be varied according to the different values of functional parameters of the fuel cell.