A method for phase correction in proton resonance frequency (PRF) thermometry application includes acquiring a series of magnetic resonance (MR) images comprising a first MR image and plurality of subsequent MR images depicting an anatomical area of interest. The MR images are acquired while tissue in the anatomical area of interest is undergoing a temperature change. Each subsequent MR image is registered to the first MR image to yield a plurality of registered images. A plurality of basis images are computed from the registered images using Principal Component Analysis (PCA). The basis images are used to remove motion-related phase changes from a second series of MR images, thereby yielding a motion corrected second series of MR images. One or more temperature difference maps are generated that depict a relative temperature change for the tissue in the anatomical area of interest based on the motion corrected second series.