A control method for a fuel cell system with a gas supplying device configured to supply fuel gas and oxidant gas to a fuel cell, includes a power generating operation step of performing a power generating operation for causing the fuel cell to generate power by controlling the fuel gas and the oxidant gas to be supplied to the fuel cell on the basis of a load required of the fuel cell. Further, the control method includes an autonomous operation step of performing an autonomous operation of the fuel cell when the load drops to or below a predetermined value. In the autonomous operation, power supply from the fuel cell system to the load is stopped and the fuel gas is passed to an anode of the fuel cell.