A method and apparatus for allocating a ranging channel for a synchronized mobile station in a wireless communication system is provided. A base station (BS) allocates the ranging channel for the synchronized mobile station in a first subframe and a first subband. An index of the first subframe and an index of the first subband are determined respectively based on an index of a second subframe and an index of a second subband in which a ranging channel of a non-synchronized mobile station is allocated.