A fuel cell system has a heater (10, 11) for heating water in the fuel cell system; and a controller (100) for controlling the heater. The controller (100) executes a stop mode having the smaller energy consumption of a temperature maintenance mode where water in the fuel cell system is maintained to a temperature greater than freezing point in a period after a shutdown the fuel cell system until a scheduled start-up date-time and a defrost start-up mode where frozen water in the fuel cell system is melted when the fuel cell system undergoes a start-up operation. The controller (100) stores a historical external temperature data for a period prior to the shutdown of the fuel cell system. The historical external temperature data is used for predicting the external temperature for the scheduled start-up date-time. The controller (100) calculates the energy consumption in the defrost start-up mode based on the predicted external temperature.