A fuel cell system in which fuel gas and oxidizing gas are supplied to a fuel cell stack and power generation is performed by electrochemical reaction between the fuel gas and the oxidizing gas, and a control method thereof are provided. This fuel cell system includes a fuel gas supply manifold which is extended in a unit cell stacking direction and which distributes the fuel gas to a fuel gas passage; a switching device which is provided inside the fuel gas supply manifold, and which switches between permission and prohibition of distribution of the fuel gas to the fuel gas passage of each of the unit cells; a load disconnect device which disconnects an output terminal of the stack from a load; a short-circuit device which short-circuits a positive electrode and a negative electrode of the output terminal of the stack; and a control device which short-circuits the positive electrode and the negative electrode of the output terminal by the short-circuit device after distribution of the fuel gas to the fuel gas passage of each of the unit cells is prohibited by the switching device when the output terminal is disconnected from the load by the load disconnect device.