A method and an apparatus for resource allocation scheduling in a wireless communication system are provided. The apparatus includes a scheduler for, if an UpLink (UL) scheduling for scheduling an allocation order of UL resources is performed prior to a DownLink (DL) scheduling for scheduling an allocation order of DL resources, setting a size α representing a size in which a DL burst region is maximally allocated in a DL sub frame, for, if the DL scheduling is performed prior to the UL scheduling, setting a size β representing a size in which the DL burst region is maximally allocated in the DL sub frame, for determining whether to discard a DL Medium Access Control (MAC) management message to be transmitted by using the size β, and for, if it is not determined to discard the DL MAC management message, determining a priority of a DL scheduling and a UL scheduling by using the size α and first performing one of the DL scheduling and the UL scheduling in accordance with the determined priority.