A method of controlling a fuel cell device includes: a step of purging a hydrogen supply unit of a fuel electrode and purging a gas supply unit of an oxidant electrode when an operation of the fuel cell device ends; a step of measuring a voltage between the fuel electrode and the oxidant electrode and determining whether the voltage is greater than a predetermined threshold; a step of continuing power generation in the fuel cell device when the voltage is greater than the predetermined threshold; and a step of depressurizing the hydrogen supply unit and the gas supply unit when the voltage is equal to or less than the predetermined threshold.