A method and an apparatus for data management through timer compensation in a wireless communication system are provided. In the method, when a data loss occurs at a first point, whether a data loss has occurred previously and so whether a timer is being driven are determined. Whether the driven timer stops or expires at a second point is determined. When the timer stops or expires at the second point, a timer value is compensated for with consideration of a time difference between the first point and the second point. A timer for the data loss of the first point is restarted based on the compensated timer value. Therefore, a delay of a retransmission request time for lost data in an RLC (Radio Link Control) layer may be minimized.