Provided are an apparatus and a method for handling a handover in multi-hop relay Broadband Wireless Access (BWA) system. In a communication method of a Relay Station (RS) in a multi-hop relay BWA system, a handover request message including a candidate node list is received from a Base Station (BS), the handover request message is sent to a Mobile Station (MS), and a handover indication message is received from the MS, the handover indication message indicating whether to perform a handover. Communication persistence can be provided for the MS having mobile characteristics, and cell load management and RS configuration/arrangement can be easily accomplished.