A fuel cell system according to the present disclosure includes: a solid oxide fuel cell that produces electricity from an electrochemical reaction by using a fuel and air and that includes a membrane electrode assembly including a proton-conductive electrolyte membrane, a cathode disposed on a first main surface of the electrolyte membrane, and an anode disposed on a second main surface of the electrolyte membrane; and a controller. In the operation stop process for stopping operation of the fuel cell system, the controller is configured to control supply of the fuel at a higher flow rate than the flow rate of the fuel consumed in the solid oxide fuel cell in an open circuit state.