There are provided an apparatus and method for controlling a fan motor. The apparatus for controlling a fan motor includes: a signal generating unit generating a pulse width modulation (PWM) input signal having a predetermined duty value; a memory storing duty correction values according to the duty value of the PWM input signal and driving characteristics of the fan motor therein; and a signal controlling unit generating a PWM output signal for operating the fan motor by using the PWM input signal and the duty correction values stored in the memory.