Apparatus and method for performing Automatic Retransmission reQuest (ARQ) in a wireless relay communication system are provided, which include performing ARQ with the base station (BS), transmitting data successfully received from the BS to mobile station (MS), and retransmitting corresponding data to the MS when a retransmission indication message is received from the BS. Since the relay station (RS) relays only the errorless data to the receiver, the reliability of the data received at the receiver can be enhanced. The load on the RS can be reduced because the transmitter controls the ARQ.