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 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 a 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 no AC impedance can be measured at the time when the predetermined time has elapsed from the scavenging start.