A method and apparatus for performing carrier management in a broadband wireless communication system supporting multiple carriers are disclosed. The method for a mobile station to perform carrier management procedure with a base station supporting multiple carriers includes receiving a carrier management command message from the base station, the carrier management command message including an action code for carrier management and a polling bit in a MAC Control Extended Header (MCEH) indicating whether an acknowledgement message is required, transmitting the acknowledgement message in response to the carrier management command message to the base station when the carrier management command message is successfully received and the polling bit is set to 1, and transmitting a carrier management indication message corresponding to the action code included in the carrier management command message to the base station.