An object is to reduce the noise and the vibration caused in operation of an injector in a non-power generation state of a fuel cell. There is provided a fuel cell system comprising fuel cells configured such that each fuel cell includes an anode, an electrolyte membrane and a cathode; an injector that is configured to supply hydrogen to the anode; and a controller that is configured to control operation of an injector to make pressure of the anode reach a target pressure. In a non-power generation state that is after a start of the fuel cell system but is before power generation of the fuel cells, the controller sets a second target pressure that is higher than a first target pressure to the target pressure and controls operation of the injector to make the pressure of the anode equal to the second target pressure. After the pressure of the anode is increased to be higher than the first target pressure, the controller sets the first target pressure to the target pressure and controls operation of the injector to make the pressure of the anode equal to the first target pressure. The first target pressure is a pressure required to supply hydrogen over the entire anodes in the fuel cell stack.