Provided are an apparatus and method of performing an uplink hybrid automatic repeat request (HARQ) in a wireless communication system. A terminal transmits a transport block to a base station via a physical uplink shared channel (PUSCH) using uplink resource allocation and receives an ACK/NACK signal for the transport block from the base station via a physical hybrid-ARQ indicator channel (PHICH). A PHICH resource used for transmitting the PHICH is identified from a PUSCH resource used for transmitting the PUSCH, and the PUSCH resource is mapped to the PHICH resource according to an uplink element carrier through which the transport block is transmitted.