A display apparatus for reducing an afterimage and a driving method thereof are provided. The display apparatus includes a video processor which divides and outputs each of frames constituting the left-eye image and the right-eye image into a plurality of sub-frames which have different sustaining times when the left-eye image and the right-eye image are input; a display unit which displays an image based on the divided sub-frames; and a controller which prevents recognition of at least one sub-frame among the plurality of sub-frames on the basis of the sustaining times of the plurality of sub-frames, thus presenting a clear image.