SOFC systems, working at high temperatures of about 800 °C, have recently attracted significant interest for application as automotive and stationary power supply systems, based on gasoline or diesel heating. For periodically changing operation, the thermal management of the system, including start‐up and load following capability, is considered a crucial point. In this work, the thermal behaviour during start‐up, operation, shut down, and restart of a simple SOFC system for mobile applications is studied. Different operating strategies, such as keeping the system at operating temperature and thermal cycling, are investigated and compared with respect to heat management, energy consumption, and start‐up performance. The characteristics depend on the system size and weight. For a 50 kWel system, with suitable insulation, immediate restart of the vehicle should be achievable for up to three days, hence no external heat is needed within that period of time. Smaller systems, e.g., Auxiliary Power supply Units (APU), replacing the conventional alternator in vehicles, cool down more rapidly. If an immediate restart is desirable ‘keeping the system at temperature’ would be the more favourable strategy.