The present invention provides an apparatus for controlling power factor compensation and method thereof, in which a turn-on timing point of a power factor compensation switch is delayed by a prescribed time from a zero crossing timing point to enhance a power factor. The present invention includes periodically detecting a zero crossing time point of an inputted voltage, turning on the power factor compensation switch if a turn-on time point of the power factor compensation switch set to a time point delayed by a prescribed time from the detected zero crossing time of the inputted voltage is reached, and turning off the power factor compensation switch if a prescribed time passes after turning on the power factor compensation switch.