The present invention relates to an apparatus and method for variable fast Fourier transform. According to an embodiment of the present invention, two n-point fast Fourier transform (FFT) processors are used to generate two n-point FFT output data or one 2n-point FFT output data. The one 2n-point input data is alternately input to the two n-point FFT processors. Each of the two n-point FFT processors selects a twiddle factor for the n-point input data or the 2n-point input data and performs fast Fourier transform. A butterfly operation is performed on signals obtained by performing fast Fourier transform on the 2n-point input data signal, and the processed signals are aligned in an output order. According to this structure, it is possible to realize a fast Fourier transform hardware engine that selectively performs multi-frequency allocation in a base station system that supports the multi-frequency allocation.