There are provided an apparatus and a method for controlling a motor. The apparatus for controlling a motor includes a signal generation unit generating a first signal indicating position information of a rotor, a counter unit sampling the first signal with a second signal different from the first signal for one period to count a sampling frequency, a memory unit storing a section counter value and an error value obtained by sampling a period immediately prior to the first signal with the second signal, and a comparison unit increasing and reducing an output signal when the sampling frequency counted by the counter unit coincides with the section counter value, wherein the comparison unit sums the sampling frequencies corresponding to error values with the sampling frequency of the first signal before the counter unit ends the sampling of one period of the first signal.