A fuel cell system includes a gas-liquid separator, a circulation flow path, a connecting flow path, and a distribution flow path. The gas-liquid separator separates fuel exhaust gas, which flows therein via a fuel exhaust gas flow path, into gas and liquid. The circulation flow path causes a gas discharge port of the gas-liquid separator and the fuel gas supply flow path to communicate with each other. The connecting flow path causes a liquid discharge port of the gas-liquid separator to communicate with the oxygen-containing gas supply flow path, via a drain valve. The distribution flow path causes the circulation flow path or a portion of the fuel gas supply flow path that is on a downstream side of a connecting section connecting to the circulation flow path to communicate with a downstream side of the drain valve of the connecting flow path via an opening and closing valve.