A fuel cell system includes a fuel cell that generates electric power using fuel gas and oxygen-containing gas and combusts fuel gas remaining unused for generation of electric power; a fuel gas supply line that supplies the fuel gas to the fuel cell; and an on-off valve disposed in the fuel gas supply line. A shutdown transition mode in which the fuel gas in the fuel gas supply line downstream from the on-off valve is supplied to the fuel cell at a flow rate smaller than that at a time of generation of electric power and is combusted therein after the on-off valve is closed, and a shutdown mode which is started after the shutdown transition mode are provided as an emergency shutdown mode in which the fuel cell undergoes emergency shutdown when the on-off valve of the fuel gas supply line is closed.