Hydrogen fuel cells are systems that can be successfully used to partially replace internal combustion propulsion systems. For this reason, the article presents an operational analysis of energy flow along with an analysis of individual energy transmission systems. Two generations of the Toyota Mirai vehicle were used for the tests. The operational analyses were carried out on the same route (compliant with RDE test requirements), assessing the system’s operation in three driving sections (urban, rural and motorway). Both generations of the drive system with fuel cells are quite different, which affects the obtained individual systems operation results as well as the overall energy flow. Research was carried out on the energy flow in the fuel cells, FC converter, battery and electric motor using a dedicated data acquisition system. The analyses were carried out in relation to the energy of fuel cells, battery energy and recovered braking energy. It was found that in the urban drive section of the second-generation system (due to its much larger mass), a slightly higher energy consumption value was obtained (by about 2%). However, in the remaining phases of the test, consumption was lower (the maximum difference was 18% in the rural phase). Total energy consumption in the research test was 19.64 kWh/100 km for the first-generation system compared to 18.53 kWh/100 km for the second-generation system. Taking into account the increased mass of the second-generation vehicle resulted in significantly greater benefits in the second-generation drive (up to 37% in individual drive sections and about 28% in the entire drive test).