A magnetic disk apparatus includes: a driving unit; and control part configured to control the driving unit. The control part includes: a position error feedback control system and a two-degree-of-freedom control system. The position error feedback control system has an integrator and a phase-lead compensator and is operative to determine a position command based on a target position and a sensed position of the magnetic head, thereby performs feedback control on the driving unit. The two-degree-of-freedom control system receives as input a target moving distance of the magnetic head and outputs a current command to the driving unit by using a mathematical model of the driving unit. The control part updates the mathematical model, and has a first update mode in which the mathematical model is updated using the output of the phase-lead compensator while the output of the integrator is provided to the driving unit.