A method and apparatus for calibrating a phased array antenna system is disclosed. The method includes receiving a first transmission signal transmitted from a transmitting antenna device, receiving a second transmission signal that is generated by the transmitting antenna device based on an unoccupied frequency band of a receiving array antenna system and a bandwidth of the frequency band, and generating a calibration matrix to calibrate a plurality of antenna elements included in the receiving array antenna system based on a signal magnitude and a phase difference which are calculated for each of the antenna elements using the first transmission signal and the second transmission signal.