A method and system for performing an inter-FA handover in a communication system are provided. An MS receives from a serving BS neighbor BS information including a BS ID of at least one neighbor BS and a reference signal index of a reference signal used in the at least one neighbor BS. When it is necessary to scan the reference signal from the at least one neighbor BS, the MS scans the reference signal corresponding to the reference signal index. If the scanned reference signal has a quality equal to or greater than a threshold, the MS determines the BS ID of the at least one neighbor BS using the reference signal index as a BS ID for a recommended neighbor BS available for the inter-FA handover.