A condensed water discharging apparatus for a fuel cell system is disclosed. The condensed water discharging apparatus includes: a drain tank installed around a hydrogen discharging line comprising an inlet portion, an outlet portion formed on both distal ends of the drain tank, and a intermediate portion having at least a drain hole installed wherein the intermediate portion is disposed inside the drain tank so that condensed water is separated from hydrogen flowing in through the intermediate portion by gravity and is drained downwardly; and a drain pump connected to the drain tank to discharge condensed water drained through the drain holes of the intermediate portion.