A method and an apparatus for supporting multiple frequency assignments in a wireless communication system are provided. An operating method of a Mobile Station (MS) for supporting multicarrier transmission in a wireless communication system includes negotiating a multicarrier operation with a Base Station (BS) during a network entry procedure, when supporting a multicarrier operation mode with the BS, sending a first control message comprising information of every multicarrier configuration supported by the MS, to the BS, receiving a second control message comprising index information of one or more carriers assigned for the multicarrier operation from the BS, and searching for configuration information of carriers corresponding to indexes of the one or more carriers assigned from the BS for the multicarrier operation.