A fuel cell system has a flooding elimination mode as one of available operation modes of fuel cells and includes a drive controller. When the ambient temperature of the fuel cell system is not higher than a preset first temperature, the drive controller causes the fuel cells to be driven in the flooding elimination mode. When the ambient temperature of the fuel cell system is not lower than a preset second temperature that is higher than the first temperature, the drive controller prohibits the fuel cells from being driven in the flooding elimination mode. On the occasion of input of a checkup instruction of the fuel cells, the drive controller causes the fuel cells to be driven in the flooding elimination mode, independently of the ambient temperature. This arrangement effectively improves the user's convenience at the checkup time of the fuel cell system having the operation mode for eliminating the state of flooding.