In a fuel cell system of the invention, a pressure regulator is provided in the pathway of a hydrogen supply conduit that connects a hydrogen tank to a fuel cell stack. An anode off gas discharged from the fuel cell stack is recirculated through a recirculation pipe into the hydrogen supply conduit. A hydrogen pump is provided in the pathway of the recirculation pipe to increase the pressure of the anode off gas. A control unit of the fuel cell system includes a hydrogen pump control module, an abnormality diagnosis module, and an atmospheric pressure-based correction module. The hydrogen pump control module regulates the rotation speed of the hydrogen pump corresponding to a power demand to be output from the fuel cell system. The abnormality diagnosis module detects an abnormal state, based on a result of determination of whether the pressure of the hydrogen supply measured by a pressure sensor is within a certain range defined by two preset threshold values. The atmospheric pressure-based correction module corrects the rotation speed of the hydrogen pump and the threshold values used for abnormality diagnosis according to the atmospheric pressure measured by an atmospheric pressure sensor. Even in the state of unstable output of the pressure regulator with a variation of the atmospheric pressure, such correction compensates for the varying flow rate of the hydrogen supply to the fuel cell stack and thus effectively prevents misjudgment of abnormality diagnosis. Namely the technique of the invention reduces the potential effect of the varying pressure of the hydrogen supply to the fuel cell system with a variation of the atmospheric pressure.