A magnetic disk apparatus includes a spindle motor for rotating a magnetic disk. Either a first pulse-train signal or a second pulse-train signal is selectively generated. The first and second pulse-train signals are different from each other in pulse frequency. When the first pulse-train signal is generated, the spindle motor is controlled to rotate at a first rotational speed in response to the first pulse-train signal. When the second pulse-train signal is generated, the spindle motor is controlled to rotate at a second rotational speed in response to the second pulse-train signal. The second rotational speed differs from the first rotational speed.