A method and an apparatus for FA switching in a wireless communication system are provided. The apparatus includes a base station for broadcasting a neighbor list, which includes a base station identifier, an FA identifier, and a preamble index corresponding to a first FA, and neighbor base station information, to mobile stations that the base station provides a service for, one of, unicasting a scanning indication message for the first FA to each of the mobile stations and broadcasting the scanning indication message to the mobile stations, for temporarily switching a second FA, which is being currently used, to the first FA, for transmitting a preamble signal corresponding to the first FA to the mobile stations by using the FA identifier and the preamble index during a preset scanning time interval, and for switching the second FA to the first FA according to a scanning result received from the mobile stations in response to the scanning indication message.