A method and apparatus for controlling an on-board charger (OBC) are provided. The method includes monitoring a voltage of an input power source, increasing or decreasing the voltage of the input power source to a preset output voltage of a power factor corrector (PFC), and operating a converter receiving the output voltage to adjust a switching frequency of the converter based on ripple current of an output terminal. Additionally, the converter includes a first switch configured to receive a first voltage of a first capacitor mounted within the PFC and a second switch configured to receive a second voltage of a second capacitor mounted within the PFC.