A bonding apparatus includes a stage on which a substrate is seated, a gantry installed above the stage, a bonding unit configured to bond a chip to the substrate while moving along the gantry, and a control part moving the bonding unit to align the bonding unit with a bonding position on the substrate, controlling the bonding unit to allow the bonding unit to bond the chip at the bonding position, determining a movement distance of the bonding unit based on a weighted sum of a number of continuous operations and an idle time of the bonding unit.