A method of shutting down a fuel cell system includes a first step of supplying hydrogen gas and air to a fuel cell stack to thereby cause the fuel cell stack to generate electricity, and a second step of stopping supply of the hydrogen gas, and then supplying air to the fuel cell stack so as to cause the fuel cell stack to generate electricity upon detection of a command to shut down the fuel cell stack. In the second step, when the pressure of the hydrogen gas is lowered to a preset lower-limit value based on an anode pressure, which actually is measured, the fuel cell stack is caused to stop generating electricity.