A fuel cell system (100) comprising: a fuel cell (1) configured to generate electric power using an oxidizing gas and a fuel gas; a recovered water tank (3) configured to store water recovered from an exhaust gas discharged from the fuel cell; a water storage tank (4) configured to store water used as cooling water for cooling the fuel cell; a water feed flow path (g) through which the water stored in the recovered water tank is supplied to the water storage tank; a pump (8) configured to force water to flow from the recovered water tank to the water storage tank within the water feed flow path; a water purifier (7) configured to purify the water forcibly flowed by said pump in the water feed flow path by means of a built-in TOC absorber (7a) before the water is supplied to the water storage tank; and a controller (101), wherein the controller controls the pump so as to operate in a stop period of the fuel cell system such that water moves in the water feed flow path.