An apparatus and method for compensating the gain of an Automatic Gain Controller (AGC) for stabilizing the reception power of discontinuously transmitted packet data in a mobile communication system are disclosed. A compensation controller receives an AGC value from the AGC, sampling the AGC value by a predetermined sample number for a predetermined period, and obtains an AGC compensation gain by comparing a predetermined value with the difference between a sampled AGC value with a reference gain for the predetermined period. A compensator compensates the AGC value with the AGC compensation gain, thereby correcting errors generated in view of the nature of the AGC.