An apparatus for controlling an ESC-integrated regenerative braking system that includes a pedal cylinder unit connected to a reservoir unit to generate a hydraulic pressure by pressing a brake pedal, a motor driven by an electrical signal output in response to a displacement of the brake pedal, a master cylinder unit connected to the pedal cylinder unit to form a hydraulic pressure for braking through a master piston moving by the driving of the motor, a control unit configured to detect a leakage of oil, based on a change in pressure in a hydraulic passage, during single-stage control, two-stage control, single-stage single-acting control, or two-stage single-acting control of the master cylinder unit, and a hydraulic control valve provided in a hydraulic passage for connecting the reservoir unit to a wheel cylinder to brake each wheel, to be opened and closed under control of the control unit.