A fuel cell system includes: a fuel cell including an anode gas flow channel and a cathode gas flow channel and generating electricity from a hydrogen-containing anode gas of the anode gas flow channel and an oxygen-containing cathode gas of the cathode gas flow channel; an anode off-gas emission path through which an anode off-gas emitted from the anode gas flow channel flows; and a cathode off-gas emission path through which a cathode off-gas emitted from the cathode gas flow channel flows. After stoppage of generation of electricity by the fuel cell, gas purging is performed in which at least a part of the cathode off-gas emission path is purged with a hydrogen-containing gas having passed through a junction where the anode off-gas emission path and the cathode off-gas emission path meet each other. The hydrogen-containing gas contains at least either the anode gas or the anode off-gas.