According to one embodiment, a magnetic disk device includes: magnetic heads; a magnetic disk in which servo patterns having different write frequencies from one another are divided and recorded into a plurality of zones; and a head controller configured such that, when performing seek control of the magnetic heads based on a model position and a model velocity obtained from a model which simulates the magnetic heads, the head controller corrects the model position and the model velocity, at the time of switching of the zones, so as to reflect variation of sampling time resulting from gaps between the zones.