To provide a fuel cell system advantageous in carrying out a flooding control even at an extended power generation operation at a low output.

The fuel cell system includes a fuel cell 1, an anode gas supply system 2 to supply anode gas to an anode electrode 10 of the fuel cell 1, a cathode gas supply system 5 to supply cathode gas to a cathode electrode 11 of the fuel cell 1, and a control portion 700 to control the anode gas supply system 2 and the cathode gas supply system 5. When continuous run time of a low-output power generation operation which tends to generate flooding elapses a first predetermined time t1, while the power generation operation is done in a way that the decline of an anode gas utilization factor in the fuel cell 1 is controlled, a first control to execute a flooding control power generation treatment for a second predetermined time t2 (t1>t2) is carried out by the control portion 700.