A fuel cell system includes: a fuel cell generating electricity when being supplied with anode gas and cathode gas; a supply channel through which the anode gas to be supplied to the fuel cell flows; a discharge channel through which anode-off gas discharged from the fuel cell flows; a discharge valve provided on the discharge channel and opened to discharge the anode-off gas; and a control section controlling opening/closing of the discharge valve. The control section calculates a valve open time of the discharge valve corresponding to a target value of a discharge amount of the anode-off gas by using an aperture ratio of the discharge channel and the target value, and closes the discharge valve based on the valve open time, the aperture ratio of the discharge channel being calculated from a first discharge amount of the anode-off gas, which is discharged by opening of the discharge valve.