An apparatus and a method are provided for operating HARQ in a mobile communication system. The method includes receiving a number of HARQ processes of a semi-persistent resource allocation and semi-persistent resource allocation interval information for a first transmission; receiving data in the first transmission at a subframe based on the semi-persistent resource allocation interval information; calculating a HARQ process IDentifier (ID) using the number of HARQ processes of the semi-persistent resource allocation, the semi-persistent resource allocation interval information, and time information; receiving control information including the HARQ process ID on an L1 control channel; receiving data in a retransmission based on the control information including the HARQ process ID; combining the data received in the first transmission and the data received in the retransmission; and decoding the combined data.