A fuel cell system includes: an AC impedance measuring unit which measures an AC impedance of a fuel cell at a scavenging start and 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 the time when the predetermined time has elapsed from the scavenging start and the predetermined time; and a limit unit which limits the scavenging execution time to a predetermined maximum scavenging time if the scavenging execution time exceeds the maximum scavenging time.