A fuel cell system including: a solid oxide type fuel cell that is supplied with an anode gas and a cathode gas to generate an electric power; a fuel tank that stores a water-containing fuel containing water; a fuel supply passage that couples the fuel cell to the fuel tank; a reformer disposed on the fuel supply passage, the reformer reforming the water-containing fuel into the anode gas; a separator disposed on the fuel supply passage in an upstream side with respect to the reformer, the separator separating the water contained in the water-containing fuel; a detector disposed in the upstream side with respect to the reformer, the detector detecting or estimating a moisture content contained in the water-containing fuel; and a control unit that controls the separator. The control unit controls the separator on the basis of the moisture content detected or estimated by the detector.