A braking control system for a vehicle is provided. The system includes a motor providing rotational force to wheels of the vehicle and a first battery storing electric energy for driving the motor. An inverter is connected to the first battery via a DC link terminal and performs a bidirectional power conversion between the DC link terminal and the motor. A DC converter is connected to the DC link terminal to down-convert a voltage of the DC link terminal and output the down-converted voltage. A second battery is supplied with the voltage converted by the DC converter and has a voltage lower than that of the first battery. A controller operates the inverter and the DC converter to charge regenerative braking energy generated from the motor during braking of the vehicle in the first battery and the second battery.