A fuel cell system is provided that can establish, for a long time period, a stack to an idling stop state. The fuel cell system includes: an idling stop control means for setting the stack to an idling stop state by, decreasing both a supplied amount of air to the stack and generated electric current produced from the stack to less than during the idling power generation; and a discharge valve control means for determining whether there is a necessity to discharge nitrogen or generated water inside of the anode system, and for opening the purge valve or drain valve in a case of there being a necessity. The discharge valve control means shortens valve open times (PO2, DO2) of the purge valve and drain valve during idling stop to less than the valve open times (PO1, DO1) thereof during idling power generation.