A fuel cell system includes a fuel cell, an operation controller, a checking unit, a scavenging unit, an instructing unit, a temperature sensor, a humidifier and a humidification controller. The operation controller selects one of a normal operation mode and a low-temperature operation mode. The checking unit determines whether the fuel cell has been started up in the low-temperature operation mode. The instructing unit provides an instruction for a shutoff of electricity generation. When the scavenging unit conducts scavenging based on the checking unit determining that the fuel cell has been started in the low-temperature operation mode in response to an instruction for a shutoff of electricity generation and an actual temperature of the fuel cell is higher than a predetermined temperature, the humidification controller controls an amount of humidification according to the actual temperature.