A fuel cell system includes a target pressure setting unit configured to periodically and repeatedly set a target upper limit pressure and a target lower limit pressure as a target pressure of anode gas and an upper limit pressure setting unit configured to set the smaller one of an upper limit value of the anode gas set based on durability performance of a fuel cell and an upper limit value of the anode gas set based on output performance of the fuel cell as an upper limit pressure of the anode gas. The target pressure setting unit sets a value smaller than the upper limit value as the target upper limit pressure when the upper limit value of the anode gas set based on the durability performance of the fuel cell is selected as the upper limit pressure of the anode gas and sets a pressure higher than the upper limit value as the target upper limit pressure when the upper limit value of the anode gas set based on the output performance of the fuel cell is selected.
