In many medical imaging modalities, the Fast Fourier Transform (FFT) is being used for the reconstruction of images from acquired raw data. The objective of the paper is to develop FFT and Inverse FT algorithms to run under GPU for performing in much faster way. The GPU based FFT implementation provides much faster reconstruction of Medical images than CPU based implementation. The GPU based algorithm is developed in MATLAB environment. GPUMat is used to running CUFFT library code in MATLAB. This work exercises the acceleration of MRI reconstruction algorithm on NVIDIA’s GPU and Intel’s Core2 Duo based CPU. The reconstruction technique shows that GPU based MRI reconstruction achieved significant speedup compared to the CPUs for medical applications at a cheaper cost.