An apparatus and method for processing received signals in a handover of a MS in a BWA communication system including a plurality of BSs capable of providing a service to the MS. According to the method, the MS receives signals of different BSs and detects preambles for each BS from the received signals. Further, the MS measures channel quality information corresponding to each of the detected preambles and compares the measured channel quality information with a preset threshold value. Further, the MS processes the signals received from the different BSs based on a result obtained by comparing the measured channel quality information with the preset threshold value.