A method for controlling a fuel cell system including a fuel cell, includes measuring an impedance of the fuel cell that includes a solid polymer electrolyte membrane to generate electric power via an electrochemical reaction between a fuel gas and an oxidant gas. An output electric current output from the fuel cell is increased to a threshold electric current value when the impedance is equal to or higher than a threshold impedance value and a target electric current value is larger than the threshold electric current value. The output electric current is maintained at the threshold electric current value. The output electric current is increased from the threshold electric current value to the target electric current value.