In this paper, we investigate the BER performance of M-ary FSK modulation system using FFT-based demodulator scheme. An explicit BER expression of the FFT demodulator scheme is analytically derived in terms of a closed form and compared with a typical demodulation scheme, the non-coherent detection method. In addition, in order to verify the derived results, the simulation results are together compared. It is noteworthy that the performance of M-ary FSK system with the FFT method is equal to that with non-coherent detection.