Design of a hybrid diesel-fuelled PEMFC system for application onboard naval ships is challenging for mul-tiple reasons. The fact that new technologies are used is only one of them. Less obvious, but also very challeng-ing is for instance choosing the ratio between installed battery capacity and fuel cell power. This ratio is a typi-cal design issue for hybrid systems. Dynamic models are necessary to find an optimal solution to this issue. In this paper the developed dynamic models are discussed, some in more detail, after which simulation results will be shown.