A fuel cell system and operation methods therefore are capable of ensuring transfer to normal operation while maintaining convenience. A fuel cell system includes a cell stack, a secondary battery, and a controller including a CPU, a main switch, and a stop button. After the main switch is turned OFF, if there is no power generation stopping command from the stop button, the CPU stops power generation in the cell stack after continuing power generation in the cell stack until a charge rate of the secondary battery becomes not lower than a first threshold value. If the charge rate is not lower than a second threshold value and is lower than the first threshold value, generation in the cell stack is stopped in response to the power generation stopping command from the stop button. If the charge rate is lower than the second threshold value, power generation in the cell stack is continued to charge the secondary battery until the charge rate becomes not lower than the second threshold value even if a normal power generation stopping command is provided from the stop button.