A method for preventing a discharge of a battery at a time of re-programming of vehicle controllers includes starting the re-programming by the vehicle controllers, turning on a high voltage relay by a battery management system (BMS) among the vehicle controllers, charging an auxiliary battery by operating a low direct current (DC) to DC converter (LDC) among the vehicle controllers, stopping a controller area network (CAN) communication between the vehicle controllers, controlling a high voltage battery by the BMS, and stopping the charging of the auxiliary battery.