A fuel cell system control method for a fuel cell system that comprises a solid-oxide-type fuel cell that has an anode gas and a cathode gas supplied thereto and that generates power in accordance with a load. The fuel cell system controls the supply of gas to the fuel cell and controls power generation. The control method includes: a power-generating operation step for controlling, in accordance with the size of the load, the amount of anode gas and cathode gas that flows to the fuel cell; and, when the load is at or below a prescribed value, an autonomous operation step for making the fuel cell perform autonomous operation. The autonomous operation step includes a gas supply step for supplying a prescribed flow of anode gas and a prescribed flow of cathode gas to the fuel cell.