Apparatus and method for allocating a Channel Quality Information CHannel (CQICH) in a wireless communication system are provided. The method includes determining CQICH patterns required for users using information of one or more users to which CQICH resources are to be allocated, and selecting a CQICH pattern block, including all of the determined CQICH patterns, from among a plurality of pre-generated CQICH pattern blocks; and allocating CQICH sub-blocks corresponding to the users' required CQICH patterns using resource layout information of the CQICH sub-blocks corresponding to the CQICH patterns of the selected CQICH pattern block, and transmitting CQICH allocation information to a Mobile Station (MS).