The present invention provides a fuel cell system capable of suppressing the accumulation of impurities in a hydrogen system even when a hydrogen pump stops. A fuel cell system 100 includes a hydrogen pump 4, which is provided in a hydrogen gas circulation flow path 3 and which circulates a hydrogen off-gas discharged from the outlet side of a hydrogen electrode 1a of a fuel cell 1 to the inlet side of the hydrogen electrode 1a, a discharge valve 61, through which the hydrogen off-gas flowing in the hydrogen gas circulation flow path 3 is discharged out of the hydrogen gas circulation flow path 3, a determination section 81, which determines whether the hydrogen pump 4 is stopped, and a control unit 80, which controls the opening/closing of the discharge valve 61. If the determination section 81 determines that the hydrogen pump 4 has been stopped, then the control unit 80 controls the opening/closing of the discharge valve 61 to increase the discharge amount of the hydrogen off-gas discharged through the discharge valve 61 so as to be greater than the discharge amount of the hydrogen off-gas discharged on the assumption that the hydrogen pump 4 is in operation.