A fuel cell system includes a fuel cell that is subjected to a purge operation of supplying an inert gas to an anode and/or cathode upon shut-down of the fuel cell. The differential pressure .DELTA.P is defined as .DELTA.P=Pa-Pc where Pa is the pressure in an inlet-side flow path leading to the anode and Pc is the pressure in an inlet-side flow path leading to the cathode. The differential pressure during the purge operation is controlled such that the differential pressure during operation .DELTA.Po and the differential pressure during the purge operation .DELTA.Pp satisfy the relation: 0<.DELTA.Po.times..DELTA.Pp. This makes it possible to reduce the stress exerted on a solid electrolyte membrane and improve the long-term reliability of the fuel cell.