This letter introduces a prime-factor Galois field Fourier transform (PF-GFFT) architecture to frequency domain decoding (FDD) of cyclic codes. Firstly, a fast FDD scheme is designed which converts the original single longer Fourier transform to a multi-dimensional smaller transform. Furthermore, a ladder-shift architecture for PF-GFFT is explored to solve the rearrangement problem of input and output data. In this regard, PF-GFFT is considered as a lower order spectral calculation scheme, which has sufficient preponderance in reducing the computational complexity. Simulation results show that PF-GFFT compares favorably with the current general GFFT, simplified-GFFT (S-GFFT), and circular shifts-GFFT (CS-GFFT) algorithms in time-consuming cost, and is nearly an order of magnitude or smaller than them. The superiority is a benefit to improving the decoding speed and has potential application value in decoding cyclic codes with longer code lengths.