A fuel cell system includes: a fuel cell; a reformer to generate a hydrogen-containing gas; an electric power generation raw material supply unit; a reforming material supply unit configured to supply at least one of reforming water and reforming air, to the reformer; an oxidizing gas supply unit to supply an oxidizing gas to a cathode of the fuel cell; a combustor to ignite an exhaust gas discharged from the fuel cell; and a controller. In an operation stop process of the fuel cell system, the controller causes the oxidizing gas supply unit to supply the oxidizing gas, causes the electric power generation raw material supply unit and the reforming material supply unit to intermittently supply the electric power generation raw material and at least one of the water and the air to the reformer, and causes the ignitor to perform an ignition operation.