A method and apparatus of generating a ranging preamble code in a wireless communication system is provided. A mobile station (MS) receives ranging channel information, and generates the ranging preamble code by selecting one of a plurality of candidate ranging preamble codes based on the ranging channel information. The plurality of candidate ranging preamble codes are based on a Zadoff-Chu (ZC) sequence of which a length is NRP and a root index is rp, and The ranging channel information comprises at least one of a start root index r0 among root indices of the plurality of candidate ranging preamble codes and a control parameter y indicating the start root index.