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 configured to put the waste gas discharge passage into an open state or a close state; a gas-liquid separator that is disposed at the hydrogen circulation passage and can separate a water component 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; a second discharge valve configured to put the water discharge passage into an open state or a close state; a control unit configured to switch the first discharge valve and the second discharge valve 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; and a liquid level sensor that is provided at the water discharge passage and is located between the gas-liquid separator and the second discharge valve, wherein the control unit puts the second discharge valve into an open state in a case where the liquid level sensor detects that a predetermined amount of water is stored in the water discharge passage, or puts the first discharge valve into a close state in a period when the second discharge valve is in an open state, and the control unit puts the second discharge valve into an open state after putting the first discharge valve into a close state in a case where the liquid level sensor detects that a predetermined amount of water is stored in the water discharge passage in a period when the first discharge valve is in an open state. 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 configured to put the waste gas discharge passage into an open state or a close state; a gas-liquid separator that is disposed at the hydrogen circulation passage and can separate a water component 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; a second discharge valve configured to put the water discharge passage into an open state or a close state; a control unit configured to switch the first discharge valve and the second discharge valve 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; and a liquid level sensor that is provided at the water discharge passage and is located between the gas-liquid separator and the second discharge valve, wherein the control unit puts the second discharge valve into an open state in a case where the liquid level sensor detects that a predetermined amount of water is stored in the water discharge passage, or puts the first discharge valve into a close state in a period when the second discharge valve is in an open state, and the control unit puts the second discharge valve into an open state after putting the first discharge valve into a close state in a case where the liquid level sensor detects that a predetermined amount of water is stored in the water discharge passage in a period when the first discharge valve is in an open state.