An automatic gain control apparatus and method of a mobile station in an OFDM system are provided. The method includes identifying a preamble section and a data symbol section in a received frame signal; when a current symbol is the preamble section, measuring a power value of a preamble signal, comparing the measured power value of the preamble signal and a threshold value, and amplifying the received frame signal based on a predetermined gain; when a data symbol section includes a pilot carrier, measuring an average power value of the pilot carrier in the data symbol, comparing the measured average power value and the threshold value, and amplifying the received frame signal based on a predetermined gain; and when the data symbol section includes no pilot carrier, maintaining an existing gain, or performing an automatic gain control operation according to a gain estimated by using the pilot carrier during the data symbol section.