A method of shutting down a fuel cell system includes a fuel cell includes generating power via an electrochemical reaction between a fuel gas and an oxidant gas. A shutdown command is output to the fuel cell to stop generating power. The fuel cell is controlled to continue generating power during an oxygen consumption process to consume oxygen in the oxidant gas remaining in a cathode system of the fuel cell even when the shutdown command is output to the fuel cell. At least one of voltage, current, and power output from the fuel cell is detected during the oxygen consumption process. Whether an abnormality occurs during the oxygen consumption process is determined based on at least one of the voltage, the current, and the power. The fuel cell is controlled to stop generating power during the oxygen consumption process when it is determined that abnormality occurs.