A fuel cell system includes: an AC impedance measuring unit which measures an AC impedance of a fuel cell at a scavenging start and which measures an AC impedance of the fuel cell at a time when a predetermined time has elapsed from the scavenging start; a scavenging execution time estimation unit which estimates a scavenging execution time based on the AC impedance measured at the scavenging start, the AC impedance measured at the time when the predetermined time has elapsed from the scavenging start, and the predetermined time; and an error processing unit which forcibly terminates scavenging processing if a fuel cell voltage becomes lower than a predetermined threshold value during a period from the scavenging start to the time when the predetermined time has elapsed from the scavenging start.