Hybridizing a fuel cell with an energy storage unit (battery or supercapacitor) combines the advantages of each device to deliver a system with high efficiency, low emissions, and extended operation compared to a purely fuel cell or battery/supercapacitor system. However, the benefits of such a system can only be realised if the system is properly designed and sized, based on the technologies available and the application involved. In this work we present a sizing-design methodology for hybridisation of a fuel cell with a battery or supercapacitor for applications with a cyclic load profile with two discrete power levels. As an example of the method's application, the design process for selecting the energy storage technology, sizing it for the application, and determining the fuel load/range limitations, is given for an unmanned underwater vehicle (UUV). A system level mass and energy balance shows that hydrogen and oxygen storage systems dominate the mass and volume of the energy system and consequently dictate the size and maximum mission duration of a UUV.