A method and apparatus for processing enhanced media data in a Digital Multimedia Broadcasting (DMB) system is provided. The apparatus for processing enhanced media data includes: a base layer processing unit configured to multiplex an elementary stream of a base layer and perform channel encoding for the multiplexed elementary stream of the base layer; an enhancement layer processing unit configured to synchronize an elementary stream of an enhancement layer with the elementary stream of the base layer and thereby multiplex the elementary stream of the enhancement layer and process the elementary stream of the enhancement layer to be transmittable via at least one of a plurality of transmission channels; and a synchronizer configured to provide the enhancement layer processing unit with synchronization information that is used for synchronizing the elementary stream of the enhancement layer with the elementary stream of the base layer.