A fuel cell system includes a fuel cell in which at least one of an anode electrode and a cathode electrode with an electrolyte membrane interposed therebetween from both sides contains a radical inhibitor; a purging device which performs a purging process of purging water in the fuel cell by supplying a purging gas into the fuel cell after a power generation stop request of the fuel cell is issued; and a purging control unit which sets a purging condition of the purging process so as to increase a purging power in stages or continuously as a correlation value correlated with an accumulated amount of the radical inhibitor accumulated in the electrolyte membrane changes with an increase in the accumulated amount.