The paper proposes a robust image alignment framework based on Fourier transform of a gradient complex image. The proposed Fourier-based algorithm can handle translation, rotation, and scaling, and it is robust against noise and non-uniform illumination. The proposed alignment algorithm is further extended to work under occlusion by partitioning the template and performing the Fourier-based alignment for all partitioned sub-templates in a voting framework. Our experiments show superior alignment results by using the proposed robust Fourier-based alignment over the previous related methods.