In a method for stopping an operation of a fuel cell system, supply of a fuel gas to an anode side of a fuel cell provided in the fuel cell system is stopped. A fuel exhaust gas discharged from the fuel cell is recirculated to the anode side of the fuel cell. An oxidant-exhaust-gas discharge path through which an oxidant exhaust gas is to be discharged from the fuel cell is sealed at a downstream position of a connecting portion at which the oxidant-exhaust-gas discharge path is connected to an oxidant-exhaust-gas recirculation path. The oxidant exhaust gas is recirculated to a cathode side of the fuel cell through the oxidant-exhaust-gas recirculation path. Recirculation of the fuel exhaust gas is stopped. Recirculation of the oxidant exhaust gas is stopped. An oxidant-gas supply path through which an oxidant gas is to be supplied to the fuel cell is sealed.