An apparatus and method for registration of a Mobile Station (MS) to a compact Base Station (BS) using Radio Frequency IDentification (RFID) in a broadband wireless communication system are provided. The method includes receiving RFID tag information of the MS from an RFID receiver, determining whether the MS is a service registration mobile station using the received RFID tag information, and if the MS is a service registration mobile station, performing a serving BS change into the compact BS for the MS and then initiating a service for the MS.