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In this paper, a mathematical model is developed to simulate the transient phenomena in a polymer electrolyte membrane fuel cell (PEMFC) system. Models currently available for a PEM fuel cell are based on either empirical or theoretic. Both models do not fully meet the need to represent static and dynamic behavior of a stack and are difficult to use in the design of PEMFC control system. Hence, a dynamic fuel cell system model is proposed in this paper which incorporates the dynamics of flow and pressure in the anode and cathode, mass/heat transfer transient features in the fuel cell body and in the auxiliary components. The model consists three distinctive models, namely, the PEM fuel cell stack model, the thermal model and the auxiliary system model. The simulation results demonstrated that this model could describe the steady state behavior and predict the transient response of cell voltage, temperature of the cell and pressures of cathode and anode channel under sudden changes in load current. The model will be very useful for the optimal design and real-time control of PEM fuel cell stack systems.