An apparatus and method are provided for quickly and finely compensating for non-repeatable run out (NPRO) of a disc drive. The NPRO compensation control apparatus in a run out compensation apparatus of a system includes: a frequency estimator directly estimating a trigonometric function value of an NRRO frequency from a predetermined signal responding to the system using a correlation between a filter coefficient of a notch filter and a notch frequency; and an NRRO compensator canceling NRRO of the system using the trigonometric function value of the NRRO frequency estimated by the frequency estimator.