A fuel cell system (FS) is provided with a fuel cell (1) having a fuel electrode (1c) and an oxidizer electrode (1a), disposed in opposition thereto, between which an electrolyte membrane (1b) is sandwiched, a fuel gas supply source (2) supplying fuel gas to the fuel cell through a fuel gas supply passage (4), a fuel gas discharge section (8, 8') discharging the fuel gas, discharged from the fuel cell, to an outside of a fuel cell system, and a control section (14) executing fuel gas substituting treatment such that, during startup of the fuel cell system, the fuel gas is discharged outside the fuel cell system through the fuel gas discharge section while supplying the fuel gas so as to cause a state quantity of the fuel gas, to be supplied to the fuel cell from the fuel gas supply source, to be constant for thereby allowing the fuel gas passage and the fuel electrode to be substituted with the fuel gas.