A fuel cell system can be initiated in shorter time while minimizing the deterioration of a fuel cell. The fuel cell system comprising a fuel cell stack comprising a plurality of laminated cells, each of the laminated cells including an electrolyte membrane interposed between a fuel electrode receiving a supply of fuel gas and an oxidizing agent electrode receiving a supply of oxidizing agent gas; a fuel gas supply device that supplies a fuel gas to the fuel electrode; an oxidizing agent gas supply device that supplies an oxidizing agent gas to the oxidizing agent electrode; a fuel electrode side discharge system that discharges a discharge gas from the fuel electrode to an external; a circulation device that recalculates the discharge gas discharged from the fuel electrode into an upstream side of the fuel electrode; a voltage limit device that limits a voltage across the fuel cell stack by drawing a current from the fuel cell stack at a time of an activation of the fuel cell system; and a controller that, at the time of the activation of the fuel cell system, halts the supply of the oxidizing agent gas to the oxidizing agent electrode, inhibits a discharge of the discharge gas to the external, and starts the supply of fuel gas to the fuel electrode when a predetermined discharge gas circulation flow quantity exists in the fuel cell system.