An apparatus and a method for operating an Automatic Repeat reQuest (ARQ) in consideration of an operation state of a Hybrid Automatic Repeat reQuest (HARQ) in a wireless communication system. In the method, when an ARQ timer expires, operation state information of a HARQ module for controlling a HARQ is determined. Whether to delay generation of Negative ACKnowledge (NACK) information in consideration of the operation state information of the HARQ module, then determined. When determining to delay the generation of the NACK information, the generation of the NACK information is delayed for a delay time determined in consideration of the operation state information of the HARQ module.