A fuel cell system comprising: a fuel cell stack configured to react hydrogen and oxygen so as to generate electricity; a hydrogen supply passage for supplying hydrogen to the fuel cell stack; a hydrogen circulation passage for returning anode waste gas discharged from an anode of the fuel cell stack to the hydrogen supply passage; a hydrogen circulation pump that is provided at the hydrogen circulation passage, has an inlet and an outlet, and operates to circulate the anode waste gas; a waste gas discharge passage for discharging the anode waste gas to outside, the waste gas discharge passage being branched from a part of the hydrogen circulation passage between the anode and the inlet of the hydrogen circulation pump; a first discharge valve (40, 41) configured to put the waste gas discharge passage into an open state or a close state; and a control unit configured to control the hydrogen circulation pump and the first discharge valve; wherein the control unit controls operation of the hydrogen circulation pump in a manner such that a pressure of the anode waste gas at the inlet of the hydrogen circulation pump becomes higher than an atmospheric pressure in the process of putting the first discharge valve into an open state, characterized by comprising a gas-liquid separator that is disposed at the hydrogen circulation passage and can separate a water component and gas included in the anode waste gas; a water discharge passage for discharging the water component separated by the gas-liquid separator to outside, the water discharge passage being connected with the gas-liquid separator; and a second discharge valve (42, 43) configured to put the water discharge passage into an open state or a close state, wherein the control unit performs control to deviate a period when the first discharge valve is in an open state and a period when the second discharge valve is in an open state from each other, the gas-liquid separator is disposed between the anode and the inlet of the hydrogen circulation pump, the water discharge passage is connected with a lower side of the gas-liquid separator, and the waste gas discharge passage is branched from the hydrogen circulation passage above the gas-liquid separator. a fuel cell stack configured to react hydrogen and oxygen so as to generate electricity; a hydrogen supply passage for supplying hydrogen to the fuel cell stack; a hydrogen circulation passage for returning anode waste gas discharged from an anode of the fuel cell stack to the hydrogen supply passage; a hydrogen circulation pump that is provided at the hydrogen circulation passage, has an inlet and an outlet, and operates to circulate the anode waste gas; a waste gas discharge passage for discharging the anode waste gas to outside, the waste gas discharge passage being branched from a part of the hydrogen circulation passage between the anode and the inlet of the hydrogen circulation pump; a first discharge valve (40, 41) configured to put the waste gas discharge passage into an open state or a close state; and a control unit configured to control the hydrogen circulation pump and the first discharge valve; wherein the control unit controls operation of the hydrogen circulation pump in a manner such that a pressure of the anode waste gas at the inlet of the hydrogen circulation pump becomes higher than an atmospheric pressure in the process of putting the first discharge valve into an open state, characterized by comprising a gas-liquid separator that is disposed at the hydrogen circulation passage and can separate a water component and gas included in the anode waste gas; a water discharge passage for discharging the water component separated by the gas-liquid separator to outside, the water discharge passage being connected with the gas-liquid separator; and a second discharge valve (42, 43) configured to put the water discharge passage into an open state or a close state, wherein the control unit performs control to deviate a period when the first discharge valve is in an open state and a period when the second discharge valve is in an open state from each other, the gas-liquid separator is disposed between the anode and the inlet of the hydrogen circulation pump, the water discharge passage is connected with a lower side of the gas-liquid separator, and the waste gas discharge passage is branched from the hydrogen circulation passage above the gas-liquid separator.