The object is to provide a simplified but highly efficient fuel cell system, permitting to perform the flame off detection and so on without supplying the burner with additional raw fuel, even if a flame rod system flame detection means is adopted as burner for reformer. The invention concerns a fuel cell system, comprising a reformer for reforming a hydrocarbon base fuel such as natural gas into hydrogen, a CO transformer, a CO eliminator, a fuel cell for generating electricity from hydrogen, and a burner for reformer for burning hydrogen gas discharged from the fuel cell and supply the reformer with heat necessary for reforming reaction, wherein the burner for reformer is provided with a flame rod system flame detection means and, at the same time, supplied with hydrogen gas containing a flame detectable amount of fuel gas.