A method for operating a fuel cell system including a fuel feeder supplying fuel, a reformer producing a hydrogen-containing gas by a reforming reaction, a fuel cell which includes a cathode and an anode, a combustor which combusts an anode off-gas discharged from the anode to produce a combustion gas, a temperature detector detecting the temperature of the combustion gas, and a storage device storing a preset target temperature profile, the target temperature profile including the temporal change in target temperature of the combustion gas in the operation of the fuel cell system, includes controlling the flow rate of the fuel supplied from the fuel feeder to the reformer in the operation such that the temperature detected by the temperature detector becomes equal to a target temperature determined on the basis of the target temperature profile.