A fuel cell system has an apparatus sending gas to the fuel cell; a part calculating an amount of residual water in the fuel cell system based on an operating and an environmental condition; a part judging whether at least one state quantity value that includes a generating duration of the fuel cell, an amount of electric power generated, and an amount of temperature change of a coolant is equal to or less than a prescribed threshold value; a part calculating a sending apparatus operating time for decreasing the residual water amount to a prescribed value; and a control part operating the gas sending apparatus until the end of the operating time, wherein the operating time calculating part calculates a different operating time depending on whether one of the state quantity values is equal to or less than a prescribed threshold value.