A fuel cell system includes a diluting apparatus which comprises a first introducing portion, a second introducing portion and an inner space and a discharge portion, and a control unit which comprises discharged fuel gas quantity detection means, a current remaining fuel gas detection means and a purge treatment means. In this fuel cell system purging the fuel gas is controlled calculating a current remaining fuel gas quantity in the inner space based on a fuel gas quantity introduced into the inner space, a flow rate of an oxidizing off-gas, a ventilation rate and a flow rate of a diluting gas.