This article describes the fundamental procedure for designing fuel cell systems for vehicle applications, especially propulsion systems. It starts with the definition of the target specifications concerning vehicle performance, derived from the driving requirements of the customer. The design process of a fuel cell vehicle is repetitive and starts with a first vehicle concept, followed by the layout of drive train, where the requirements concerning fuel consumption, emissions, acceleration, top speed and climbing ability must be considered. The design procedure of the fuel cell system consists of the concept phase, the modeling phase as well as the simulation phase. The results, which include efficiency, emissions, turn‐down ratio, weight, volume, costs, cold start‐up time and heat rejection, are then compared with the original specifications. For a detailed simulation, input data and boundary conditions are necessary at the start, which can only result from the total design process — so these data have to be estimated before starting the layout process. The data found in the simulation of the fuel cell system are re‐used within the vehicle simulation. Analysis shows the sensitivity of the system concerning changes of a given technology and leads to the final definition of the design of all components of the drive system.