A method and an apparatus for switching a Frequency Assignment (FA) by a base station in a wireless communication system are provided. The method includes, upon detecting movement of the base station, communicating with a mobile terminal using a first FA via a first FA-transceiver among a plurality of FA-transceivers which process signals transceived via each of the plurality of FAs, and selecting, upon detecting a change in a wireless environment caused by the movement, a second FA from among the plurality of FAs, operating a second FA-transceiver which processes signals transceived via the second FA, transmitting, to the mobile terminal, a scanning-instructing message for instructing the reference signal transmitted via the second FA to be scanned, and switching the first FA to the second FA in accordance with the result of the scanning received from the mobile terminal in response to the scanning-instructing message.