Provided are a fuel cell system capable of shortening the wait time of an observer who confirms set points of a system interconnection protective device before starting a system interconnection operation, and a method for operating the fuel cell system.A fuel cell system 100 includes: a hydrogen generating unit 16 configured to generate a hydrogen-containing gas by using a raw material; a heater 18 configured to heat the hydrogen generating unit; an electric power generation start command unit 32 configured to receive a command of start of an electric power generating operation of the fuel cell system, the command being input by a manual operation of an operator, the electric power generating operation being interconnected with an electric power system; and a controller 28 configured to: execute electric power generation stand-by, in which the fuel cell system stands by for the start of the electric power generating operation interconnected with the electric power system, while executing a temperature maintaining process of the hydrogen generating unit by the heater after completion of a temperature increasing process of the hydrogen generating unit by the heater; and when the electric power generation start command unit receives the command of the start of the electric power generating operation, stop the electric power generation stand-by and start the electric power generating operation interconnected with the electric power system.