According to one embodiment, a magnetic disk device includes a disk, a first head, a second head, an actuator configured to position the first head and the second head over the disk, and a controller configured to control the actuator based on a first value having a first waveform suppressing a disturbance component, wherein the controller is configured to invert, in the first waveform, a polarity of a third waveform succeeding a first timing with respect to a polarity of a second waveform preceding the first timing in a case where the first head is changed to the second head at the first timing.