An over-the-air update apparatus in a vehicle and a method thereof are provided. The over-the-air update apparatus in the vehicle includes a communication device that receives data for an over-the-air (OTA) update of vehicle software from an external server and a processor that determines a priority for the over-the-air update based on a current consumption and a data processing speed with respect to each of a plurality of controllers. The processor allows data to be selectively transmitted based on the determined priority.