A method for controlling a fuel cell system is a method for controlling a fuel cell system including a solid oxide fuel cell which generates a power upon receiving supplies of an anode gas and a cathode gas. The method for controlling the fuel cell system includes; as a stop control of the fuel cell, stopping a supply of the anode gas while continuing a supply of the cathode gas to the fuel cell, and shutting off a discharge side of an anode of the fuel cell; and carrying out an additional control to supply the anode gas to the fuel cell during the stop control and/or an additional control to decrease the flow rate of the cathode gas during the stop control.