A method and apparatus for managing multiple Timing Advance Groups (TAGs) operating with different timings are provided for use in a Long Term Evolution (LTE) system. The method for managing multiple TAGs at a base station of a wireless communication system supporting carrier aggregation according to an exemplary embodiment of the present invention includes categorizing a plurality of carriers into at least one TAG according to a predetermined rule, assigning a TAG index to each TAG, transmitting the TAG index to a terminal, generating a Timing Advance Command (TAC) for synchronization, and transmitting the TAC to the terminal in a random access process. The method and apparatus for managing TAGs according to exemplary embodiments of the present invention is capable of informing of the timing advance group to which each carrier belongs and managing multiple timing advance groups efficiently without signaling overhead.