The present invention relates to a transmitter of an OFDMA system capable of controlling a gain for variation of subchannel allocation, and a method thereof. The transmitter includes a subchannel number determining unit, a modulator, a digital/analogue converter, and a gain controller controlling the gain. The subchannel number determining unit determines the number of subchannels in use according to communication environments, and the modulator modulates transmission data with reference to the number of subchannels determined by the subchannel number determining unit and outputs the modulated transmission data. The digital/analogue converter converts the transmission data into analogue data and transmits the converted analogue data through a transmit antenna. The gain controller controls gains of the transmission data according to gain values corresponding to the number of subchannels.