A calibration apparatus of a portable terminal capable of performing calibration without disassembling a case of the portable terminal without a cable insertion hole in the case, and a system thereof are provided. The calibration system includes a calibration jig, including a cable coupler in which a Radio Frequency (RF) cable is inserted, for insertion in a user identification card slot unit of the portable terminal which connects a wireless path between an RF communication unit of the portable terminal and the calibration jig, and blocks a second wireless path between the RF communication unit and an antenna, a measuring device for connecting with the calibration jig through the RF cable, and for exchanging a wireless signal with the RF communication unit through the first wireless path, and a computer for connecting with the measuring device and the portable terminal, and for controlling a calibration procedure of the portable terminal.