A method for operating a fuel cell system having a fuel cell equipped with an anode and a cathode includes the steps of generating electric power by allowing hydrogen gas supplied to the anode and oxygen gas supplied to the cathode to react electrochemically with each other, recovering water from water vapor discharged from at least one of the anode and cathode, storing recovered water in a water storing portion equipped with a tank having a closable drain opening, through which opening water stored in the tank is dischargeable to outside the fuel cell system, supplying water stored in the tank to a water utilizing means by a water supply portion, and making a decision whether or not to discharge the stored water to outside the fuel cell system through the drain opening in view of an increase in an amount of undesirable germs contained in water stored in the water storing portion.