According to one embodiment, a magnetic disk device includes a first disk, the second disk, and a first head which writes and reads to the first disk, a second head which writes and reads to the second disk, and a controller which calculates an estimated position at which the second head is estimated to be disposed on the second disk based on first relative position information related to a relative position in a radial direction between the first head and the second head when the first head is switched to the second head.