A method for controlling a fuel cell vehicle is provided. The method includes setting a target purge degree of an anode gas and a target opening degree of an air pressure control valve and determining whether a fuel cell stack is in a power generation stop state. When the fuel cell stack is in the power generation stop state, when the anode gas is purged from the anode based on the target purge degree and the target opening degree, whether hydrogen in the anode gas will flow backwards to a stack enclosure is determined. When the hydrogen flows backwards, at least one of the target purge degree and the target opening degree to a level at which the backflow of the hydrogen is prevented is modified, and the anode gas from the anode based on the modified target purge degree and the modified target opening degree is purged.