A fuel cell system including: a fuel cell including a fuel gas channel and an oxidant gas channel, which is configured to generate electricity using a fuel gas and an oxidant gas; a diluting unit configured to dilute gas discharged from the fuel gas channel by mixing the discharged gas with a dilution gas which is supplied from an oxidant gas supply unit and passed through and discharged from the fuel cell, and to exhaust the diluted gas to outside; a purge valve configured to purge gas in the fuel gas channel to the diluting unit; a scavenging unit configured to scavenge the fuel gas channel and the oxidant gas channel; and a dilution assist unit configured to supply a dilution assist gas to the diluting unit through an assist passage connected to the diluting unit to assist dilution in the diluting unit, during scavenging by the scavenging unit.