Provided are an apparatus and method for controlling a motor which compensates for a mechanical tolerance of the motor in a case where a feedback sampling frequency increases in order to more precisely control a brushless DC motor. The apparatus for compensating the mechanical tolerance of the brushless DC motor includes: a speed controller calculating a speed error that is a difference between a motor speed measured in control sections and a reference speed using a back electromotive force generated by the motor, and generating a motor control input signal using the speed error of the control section; a moving average calculator calculating a moving average value of the motor control input signals in a predetermined moving average section including recently generated motor control input signal whenever the motor control input signals are generated; and a motor driver generating an electric current for driving the motor corresponding to the moving average value.

 
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