The present disclosure provides a system and a method for controlling kick-back in an electric booster type brake system capable of reducing a kick-back phenomenon in which a hitting force is transmitted to a brake pedal due to a difference between a high braking hydraulic pressure already generated in a power piston of a second master cylinder by driving a motor and a low braking hydraulic pressure generated in a first master cylinder when a driver steps on a brake pedal, in a fall back situation in which electric power is not smoothly supplied to the motor due to a low voltage of a battery.