For cooperative transmission in a broadband wireless communication system, an apparatus and operating method of a Base Station (BS) in a broadband wireless communication system are provided. The method includes receiving a cooperative transmission REQuest (REQ) message which includes at least one of information designating a cooperative Mobile Station (MS), a pilot pattern of the cooperative MS, a variable determining a permutation pattern, and an orthogonal code of the cooperative MS, from a control station, allocating a resource of a predefined Coordinated MultiPoint transmit/receive (CoMP) zone occupying part of a frame, to at least one cooperative MS designated by the cooperative transmission REQ message, and communicating with the at least one cooperative MS according a cooperative transmission scheme using the resource of the CoMP zone.