A method and apparatus for performing a carrier management in a broadband wireless communication system supporting multi-carriers are disclosed. A method for a mobile station to perform a carrier management procedure with a base station supporting multiple carriers includes receiving a carrier management command message including an action code indicating a primary carrier change and an action time, on a serving primary carrier, transmitting an acknowledgement message indicating that the carrier management command message is successfully received in the mobile station, on the serving primary carrier, and switching the primary carrier to a target carrier indicated by the carrier management command message at the action time, wherein the action time is set to a value more than a retransmission timer, the retransmission timer is set to a time during which the base station waits for receiving the acknowledgement message in response to the carrier management command message.