Disclosed are an apparatus and method for controlling a Direct Current (DC)/DC converter which controls energy flow between a first DC source and a second DC source to eliminate a high-frequency resonance. The apparatus for controlling the DC/DC converter includes a voltage controller, one or more subtractors, one or more fundamental component current controllers, a first coordinate transformer, a resonance current component extractor, a resonance frequency tracker, one or more resonance component current controllers, a second coordinate transformer, one or more adders and a Pulse Width Modulation (PWM) signal generation unit. The method implemented by the apparatus can effectively control any high-frequency resonance current components generated in the DC/DC converter.