A motion estimation apparatus according to an aspect of the present invention is a motion estimation apparatus for estimating, using a set of multi-focus images which correspond to a single scene and have different focuses, motion for each of the first regions included in the scene, including: a cost value computing unit configured to compute, using the set of multi-focus images, for each of the first regions, a cost value indicating a difference between a blur amount of the first region and a standard blur amount determined for each of distances in a depth direction; and a motion estimation unit configured to estimate, using the cost value, the motion of the first region corresponding to the cost value.