A fuel cell system can be initiated in shorter time while minimizing the deterioration of a fuel cell. The fuel cell system includes a fuel cell stack having a fuel electrode, an oxidizer electrode and an electrolyte membrane disposed there between, the fuel cell producing electricity by an electrochemical reaction of a fuel gas and an oxidizer gas, which are supplied to the fuel electrode and the oxidizer electrode, respectively; a fuel gas supplying device for supplying the fuel gas to the fuel cell stack; an oxidizer gas supplying device for supplying the oxidizer gas to the fuel cell stack; a current controlling device for extracting a current from the fuel cell stack; and a voltage sensor disposed in at least two of the fuel cell stacks. A controller controls the current controlling device such that a minimum voltage, which is obtained from the voltage sensor after a fuel gas is supplied to the fuel electrode without supplying the oxidizer gas to the oxidizer electrode at the time of initiating, becomes zero volts or more. Then, the oxidizer gas is supplied to the oxidizer to start producing electricity.