To provide a fuel cell system to enable to make a fuel cell suitably scavenged.

This is the fuel cell system 1 provided with the fuel cell 2 which has a fuel gas flow passage 4 and an oxidizer gas flow passage 5, and generates power because the fuel gas is supplied to the fuel gas flow passage 4 and the oxidizer gas is supplied to the oxidizer gas flow passage 5 respectively, a piping 21a connected to the downstream end of the fuel gas flow passage 4, a gas-liquid separator 21 which is connected to the downstream end of an off-gas piping 21a and gas-liquid separates the off gas, the piping 21a which is connected to the gas-liquid separator 21 and returns the gas-liquid separated gas to the fuel gas supplying side of the fuel cell 2, pipings 24a, 24b which are connected to the piping 24a and in which the off gas is circulated during scavenging of the fuel cell 2, and a scavenging valve 24 which is installed at the scavenging off-gas pipings 24a, 24b and opened in scavenging the fuel cell 2, and a pressure loss of the scavenging valve 24 side from a contact point C of the piping 21a and the piping 24a is smaller than that of the gas-liquid separator 21 side from the contact point C.