In this paper the dynamics of a polymer electrolyte membrane (PEM) fuel cell system and its associated power electronics are modelled and simulated. The fuel cell system model includes the dynamics of reactant flow, membrane resistance and charge, double layer capacitance as well as steady state equations. The DC Output of the 5 kW fuel cell stack is converted to 120 V, 60 Hz AC by a pulse width modulated inverter. The inverter output is held constant by a PID controller. Matlab‐Simulink™ and Power System Blockset (PSB) are used for the modelling and simulation of the fuel cell generator. The effects of load variation on output voltage, current, and fuel cell reactant flows are investigated. Simulation results indicate that variations in the systems electrical and physical parameters are within acceptable limits. Such a fuel cell generator could be used in grid connected and stand‐alone applications.