Chiral amino boronic acids and their derivatives have a wide range of applications including enzyme inhibitors, anti-cancer agents and molecular sensors. They also draw attention as effective catalysts. Recently, a new proline based amino boronic acid derivative, homoboroproline, was synthesized and demonstrated to be an efficient catalyst in an asymmetric aldol reaction. The reaction mechanism has been elucidated in the present study for the first time. Considering different orientations of the enamine intermediate and the aldehyde, potential alternative mechanisms were modeled with density functional theory (DFT) calculations via PCM/M06-2X/6-31G(d,p) method in acetone. The potential energy surface of each mechanism was explored to establish the rate-determining and enantioselectivity-determining steps. The calculated enantiomeric excess values (>99%) were found to be in agreement with the experimental values (93%, 95%). The detailed investigation of the transition state structures of the selectivity-determining step has revealed that attractive interactions between boron and aldehyde oxygen are responsible for the selectivity confirmed by natural bond orbital (NBO) analysis. The results provide insight into the origin of enantioselectivity in asymmetric aldol reaction catalyzed by homoboroproline.