A disk drive is disclosed comprising a plurality of disk surfaces, and a plurality of heads actuated over the respective disk surfaces. In one embodiment, control circuitry generates a pulse duty cycle signal for one of the heads. In another embodiment, the control circuitry generates a first pulse width modulated signal for a first head, and a second pulse width modulated signal for a second head, wherein the second pulse width modulated signal comprises a phase offset from the first pulse width modulated signal.