Provided are a high-speed Discrete Fourier Transform (DFT) apparatus and a method thereof. The high-speed DFT apparatus includes a zero padding unit, a Fast Fourier Transform (FFT) unit, and a preamble index decision unit. The zero padding unit receives a first input signal having a length of a prime number and changes the first input signal into a second input signal having a length of an exponentiation of 2. The FFT unit performs a FFT on the second input signal outputted from the zero padding unit. The preamble index decision unit detects a preamble index from an output signal from the FFT unit.