A method and apparatus for performing a carrier management in a broadband wireless communication system supporting multi-carriers are discussed. According to an embodiment, a method for a mobile station to perform a carrier management procedure with a base station supporting multiple carriers, includes receiving, by the mobile station from the base station, an instruction for a primary carrier change; transmitting, by the mobile station to the base station, an acknowledgement message indicating that the instruction is successfully received; and changing, at a specific time, a current primary carrier to one of the multiple carriers within the base station, wherein the specific time is determined based on the instruction.