A system and a method for switching mobile station identification information in a wireless communication system are provided. The method includes sending, at a base station, a RNG-ReSPonse (RSP) message including a temporary mobile station identifier to the mobile station, determining, at the mobile station, the temporary mobile station identifier in the RNG-RSP signal, when base station receives REGistration (REG)-REQ message including the temporary mobile station identifier from the mobile station, sending, at the base station, a REG-RSP message to the mobile station, determining, at the mobile station, the mobile station identifier in the REG-RSP message and sending a response signal for the REG-RSP message to the base station, when receiving the response signal for the REG-RSP message, deleting, at the base station, the temporary mobile station identifier of the mobile station, and communicating, at the mobile station and the base station, using the mobile station identifier.