An apparatus and method for reducing a Peak to Average Power Ratio (PAPR) of a Secondary Advanced (SA) preamble in a wireless communication system are provided. A method for transmitting an SA preamble includes determining an SA preamble, constructed in a unit of subblocks, according to a frequency band to be used for transmitting information, determining a sequence for reducing a PAPR of the SA preamble in consideration of at least one of a frequency band, a segment IDentifier (ID), and the number of antennas transmitting the SA preamble, updating the SA preamble using the determined sequence, and transmitting the updated SA preamble to a receive end.