A fuel cell system, comprising: a fuel cell stack; a cathode supply flow passage which is connected to the fuel cell stack and through which cathode gas flows; a cathode off-gas flow passage which is connected to the fuel cell stack and discharges cathode off-gas; a bypass flow passage which is branched off from the cathode supply flow passage, joins the cathode off-gas flow passage, and through which a part of the cathode gas flows while bypassing the fuel cell stack; a bypass valve configured to regulate a bypass flow rate in the bypass flow passage; and an anode off-gas flow passage which is connected to the fuel cell stack and discharges anode off-gas; wherein: the anode off-gas flow passage joins the bypass flow passage at a side downstream of the cathode off-gas flow passage or the bypass valve; a housing of the bypass valve is formed with an atmosphere communication hole allowing communication between the interior of the housing and atmosphere and having a possibility of causing the anode off-gas flowing back in the bypass flow passage to flow out to the atmosphere; and the bypass valve is formed with a clearance configured to leak a predetermined quantity of gas, and the clearance is so provided that the predetermined quantity is larger than an external leakage quantity leaking to the atmosphere from the atmosphere communication hole even when the bypass valve is in a fully closed state. a fuel cell stack; a cathode supply flow passage which is connected to the fuel cell stack and through which cathode gas flows; a cathode off-gas flow passage which is connected to the fuel cell stack and discharges cathode off-gas; a bypass flow passage which is branched off from the cathode supply flow passage, joins the cathode off-gas flow passage, and through which a part of the cathode gas flows while bypassing the fuel cell stack; a bypass valve configured to regulate a bypass flow rate in the bypass flow passage; and an anode off-gas flow passage which is connected to the fuel cell stack and discharges anode off-gas; wherein: the anode off-gas flow passage joins the bypass flow passage at a side downstream of the cathode off-gas flow passage or the bypass valve; a housing of the bypass valve is formed with an atmosphere communication hole allowing communication between the interior of the housing and atmosphere and having a possibility of causing the anode off-gas flowing back in the bypass flow passage to flow out to the atmosphere; and the bypass valve is formed with a clearance configured to leak a predetermined quantity of gas, and the clearance is so provided that the predetermined quantity is larger than an external leakage quantity leaking to the atmosphere from the atmosphere communication hole even when the bypass valve is in a fully closed state. the anode off-gas flow passage joins the bypass flow passage at a side downstream of the cathode off-gas flow passage or the bypass valve; a housing of the bypass valve is formed with an atmosphere communication hole allowing communication between the interior of the housing and atmosphere and having a possibility of causing the anode off-gas flowing back in the bypass flow passage to flow out to the atmosphere; and the bypass valve is formed with a clearance configured to leak a predetermined quantity of gas, and the clearance is so provided that the predetermined quantity is larger than an external leakage quantity leaking to the atmosphere from the atmosphere communication hole even when the bypass valve is in a fully closed state.