Provided is a fuel cell system capable of preventing a fuel cell from being polarized at a high potential for a long time during start-up. A fuel cell system 1 includes a first injector 23A and a second injector 23B in a fuel gas inlet passage. When an ECU 60 determines that a power generation down time is equal to or more than a predetermined period at start-up of a fuel cell stack 10, a target pressure of hydrogen supplied to an anode passage 12 is set to be higher for supply than when the power generation down time is less than the predetermined period. In addition, as the power generation down time of the fuel cell stack 10 becomes longer, the target pressure is set to be higher. Also, a pressure increase in the fuel cell stack is set to be lower than that during ordinary power generation.