An apparatus and method for guiding deactivation of a battery sensor of ISG vehicles is capable of informing a driver of operation prohibition when the battery sensor mounted on the ISG vehicles is deactivated. The apparatus for guiding deactivation of a battery sensor of ISG vehicles includes a display unit displaying that the battery sensor is deactivated; and an engine control unit determining whether the battery sensor normally operates or not, and controlling a display operation of the display unit based on the determination result.