Provided is a fuel cell system capable of ensuring that the fuel cell system can start next time and preventing scavenging processing from being continued for an unnecessarily long time. An impedance comparator 150 compares an impedance reference value ins stored in a memory 151 with a measured impedance stored in a measurement memory 152, and determines whether or not the amount of water remaining in the system falls below a threshold value. On the other hand, an SOC comparator 170 compares an SOC reference value stored in a memory 171 with a detected SOC stored in an SOC memory 172, and determines whether or not the detected SOC falls below the SOC reference value. A scavenging control section 160 performs scavenging control based on both of the determinations above.