A braking control system and a method for an eco-friendly vehicle are provided to resolve discrepancy in braking force occurring during switching between hydraulic braking and regenerative braking. The system includes a deceleration determiner that determines target and actual decelerations of the vehicle based on collected information when braking and a torque calculator that calculates target and actual deceleration torques from the determined target and actual decelerations of the vehicle using vehicle equivalent inertia information. An error calculator calculates a torque error and a torque corrector corrects a pre-correction target regenerative braking torque by the calculated torque error and calculates a post-correction target regenerative braking torque. A motor controller adjusts a regenerative braking torque of a motor according to the calculated post-correction target regenerative braking torque.