A fuel cell system that supplies an anode gas and a cathode gas to a fuel cell to cause the fuel cell to generate an electricity. The fuel cell system includes a high pressure tank, an anode gas supply passage configured to supply the anode gas to the fuel cell from the high pressure tank, an anode pressure control valve disposed on the anode gas supply passage, the anode pressure control valve adjusting an anode gas pressure of the fuel cell, an anode gas valve disposed between the high pressure tank and the anode pressure control valve, the anode gas valve adjusting a source pressure of the anode pressure control valve, and a valve control unit configured to control to open and close the anode pressure control valve and the anode gas valve on the basis of an operating state of the fuel cell system. The valve control unit controls the anode pressure control valve and then closes the anode pressure control valve after the valve control unit closes the anode gas valve such that a first pipe pressure becomes less than a predetermined pressure before the fuel cell system is stopped, the first pipe pressure being a pressure inside a first pipe between the anode gas valve and the anode pressure control valve in the anode gas supply passage. The valve control unit opens the anode pressure control valve at an activation of the fuel cell system. The predetermined pressure is smaller than a pressure that degrades a durability of the fuel cell at the activation of the fuel cell system.