A fuel cell system includes a fuel cell, a fuel gas supply channel, a fuel off-gas discharge channel, an oxidant gas supply channel, an oxidant off-gas discharge channel, a first shut valve, a second shut valve, a shut valve controller, a temperature detector, a scavenging device, and an elapsed-time detector. The elapsed-time detector is configured to detect an elapsed time elapsed from a timing at which the fuel cell is shut down. The scavenging device scavenges the oxidant gas flow channel and the fuel gas flow channel in sequence if the elapsed time detected by the elapsed-time detector is within a first predetermined period of time. The scavenging device scavenges the fuel gas flow channel and the oxidant gas flow channel in sequence if the elapsed time detected by the elapsed-time detector is outside the first predetermined period of time.