In a magnetic field distortion calculation apparatus, method, and program, information of magnetic field distortion inside a subject can be accurately acquired.An image acquisition unit acquires a reference image and a three-dimensional image of the head of the subject. A feature point detection unit detects a plurality of feature points from the three-dimensional image, and a virtual feature point estimation unit estimates a plurality of virtual feature points, which are to be present in the brain in the three-dimensional image, using the plurality of feature points. A magnetic field distortion information acquisition unit acquires magnetic field distortion information, which indicates spatial magnetic field distortion caused by a three-dimensional image capturing apparatus included in the three-dimensional image, by performing registration between the plurality of feature points and the plurality of virtual feature points and a plurality of reference points.