A fuel cell system comprising: a fuel cell stack having a plurality of cells each having hydrogen channels through which hydrogen gas flows, a hydrogen channel inlet that allows the hydrogen gas to flow into the hydrogen channels, and a hydrogen channel outlet that allows the hydrogen gas to flow out from the hydrogen channels; a main load to which electric power is supplied from the fuel cell stack; a circulation passage that connects the hydrogen channel inlet with the hydrogen channel outlet, such that the hydrogen gas supplied to the fuel cell stack is circulated through the circulation passage; a hydrogen pump provided in the circulation passage and configured to rotate in a selected one of a positive direction corresponding to a normal feeding direction of the hydrogen gas, and a negative direction opposite to the positive direction; and a controller configured to control the hydrogen pump, wherein the controller is configured to rotate the hydrogen pump in the positive direction so as to feed the hydrogen gas in a predetermined first hydrogen amount into each of the cells through the hydrogen channel inlet, at a first hydrogen flow rate that is larger than a minimum hydrogen flow rate required for power generation, and then rotate the hydrogen pump in the negative direction so as to feed the hydrogen gas in a second hydrogen amount that is smaller than the first hydrogen amount, into each of the cells through the hydrogen channel outlet, during a period from a time when supply of electric power from the fuel cell stack to the main load is stopped, to a time when supply of electric power to the main load is started next time. a fuel cell stack having a plurality of cells each having hydrogen channels through which hydrogen gas flows, a hydrogen channel inlet that allows the hydrogen gas to flow into the hydrogen channels, and a hydrogen channel outlet that allows the hydrogen gas to flow out from the hydrogen channels; a main load to which electric power is supplied from the fuel cell stack; a circulation passage that connects the hydrogen channel inlet with the hydrogen channel outlet, such that the hydrogen gas supplied to the fuel cell stack is circulated through the circulation passage; a hydrogen pump provided in the circulation passage and configured to rotate in a selected one of a positive direction corresponding to a normal feeding direction of the hydrogen gas, and a negative direction opposite to the positive direction; and a controller configured to control the hydrogen pump, wherein the controller is configured to rotate the hydrogen pump in the positive direction so as to feed the hydrogen gas in a predetermined first hydrogen amount into each of the cells through the hydrogen channel inlet, at a first hydrogen flow rate that is larger than a minimum hydrogen flow rate required for power generation, and then rotate the hydrogen pump in the negative direction so as to feed the hydrogen gas in a second hydrogen amount that is smaller than the first hydrogen amount, into each of the cells through the hydrogen channel outlet, during a period from a time when supply of electric power from the fuel cell stack to the main load is stopped, to a time when supply of electric power to the main load is started next time.