In this paper the performance of two polymeric electrolyte fuel cell systems (FCS) for hybrid power trains are presented and discussed. In particular, an experimental analysis was effected on 2.4 and 20 kW stacks with the aim to investigate the energy management issues of the two FCSs for utilization as power sources in electric power trains for scooter and minibus, respectively. The stack characterizations permitted the effect of the main operative variables (temperature, pressure and stoichiometric ratio) on mean power density of cells to be evaluated. The FCS efficiency was evaluated and compared for the two traction systems, individuating the optimal operative conditions for automotive application and specifying the energy losses of the auxiliary components. The efficiency of both fuel cell systems resulted higher than 40% in a wide range of loads (100–600 mA/cm2), with maximum values close to 50%. The experimental characterization of the two power trains was carried out on dynamic test benches, able to simulate the behaviour of the two vehicles on the European R40 driving cycle. The characterization of the two propulsion systems on R40 driving cycle evidenced that the overall efficiency was not affected significantly by the hybrid configuration adopted, as the efficiency values ranged from 27 to 29% in the different procedures analyzed.