A fuel cell system, comprising: a fuel cell stack including a stacked body provided by stacking a plurality of cells in a stacking direction; a compressor configured to feed a purge gas to a cathode of the fuel cell stack; a controller configured to control the compressor, such as to perform stop-time purging that purges the cathode of the fuel cell stack when operation of the fuel cell system is stopped; a first temperature gauge configured to measure a first temperature value that reflects temperature of a cell placed near a center in the stacking direction among the plurality of cells constituting the stacked body and to input the measured first temperature value into the controller; and a second temperature gauge configured to measure a second temperature value that reflects temperature of a cell placed near an end in the stacking direction among the plurality of cells constituting the stacked body and to input the measured second temperature value into the controller, wherein the controller is configured to suspend the stop-time purging when the first temperature value is equal to or higher than a first reference temperature and the second temperature value is lower than a second reference temperature.