This paper studies the transient response of the output voltages of a Ballard-Mark-V 35-cell 5kW proton exchange membrane fuel cell (PEMFC) stack with power conversion for applications in autonomous underwater vehicles (AUVs) under load changes. Four types of pulse-width modulated (PWM) dc–dc power converters are employed to connect to the studied fuel cell in series for converting the unregulated fuel cell stack voltage into the desired voltage levels. The fuel cell model in this paper consists of the double-layer charging effect, gases diffusion in the electrodes, and the thermodynamic characteristic; PWM dc–dc converters are assumed to operate in continuous-conduction mode with a voltage-mode control compensator. The models of the study's fuel cell and PWM dc–dc converters have been implemented in a Matlab/SIMULINKTM environment. The results show that the output voltages of the studied PEMFC connected with PWM dc–dc converters during a load change are stable. Moreover, the model can predict the transient response of hydrogen/oxygen out flow rates and cathode and anode channel temperatures/pressures under sudden change in load current.