A dynamic simulation of a PEMFC hybrid system has been developed in a MATLAB/SIMULINK environment to study the component interactions between a diesel fuel processor, a PEMFC system, a compressor/expander system, and a battery pack. Each subsystem has been modeled using its fundamental reactions or processes. The simulation also allows subsystem performance to be analyzed and control strategies to be developed and tested for a range of configurations. This paper describes the models used in the dynamic simulation tool and how these models are programmed and implemented in the MATLAB/SIMULINK environment. The paper also presents the results from a study of a PEMFC marine system as an auxiliary power source for a ship hotel load to illustrate the capability of the simulation tool. The analysis focuses on the effect of using a fuel cell stack and a diesel fuel processor with 36 tonnes of high-temperature LAIS (lithium-aluminium/iron sulphide) battery pack on the performance of the system under the hotel load duty cycle. A steady-state analysis was performed for the average system power of , and the results of steady state calculations are also presented.