A method of maintaining a calibrated DC fan motor is provided in which normal operation of the motor is periodically and temporarily suspended in order to calibrate the motor. During normal operation, the motor controller selects an appropriate PWM control signal to achieve the desired motor speed. This PWM control signal is later modified during the calibration process on the basis of the difference between the desired motor speed and the actual motor speed, where the actual motor speed is determined by temporarily interrupting power to the motor, measuring the back EMF of the motor, and calculating the actual motor speed based on the back EMF. When normal operation is resumed, the motor controller uses the modified PWM control signal.