An apparatus for controlling a power factor correction circuit of a charger for charging a vehicle batter is configured to correct a power factor of an input AC voltage through switching of a switching element. The apparatus for controlling the power factor correction circuit includes: a phase angle detection unit configured to detect phase angle information of the input AC voltage; and a frequency determination unit configured to synchronize a period in which a preset frequency variation value varies, with a period of the input AC voltage by applying the phase angle information to the frequency variation value, and determine, as a switching frequency of the switching element, a value obtained by applying the synchronized frequency variation value to a preset fundamental frequency value.