A bonding apparatus includes an upper holding unit, a lower holding unit, a pushing unit and an attracting/holding unit. The upper holding unit is configured to hold a first substrate from a top surface thereof which is a non-bonding surface. The lower holding unit is provided under the upper holding unit and is configured to hold a second substrate from a bottom surface thereof while allowing the second substrate to face the first substrate. The pushing unit is configured to press a central portion of the first substrate from above to bring the central portion of the first substrate into contact with the second substrate. The attracting/holding unit is configured to be moved up and down with respect to the upper holding unit and hold a part of the top surface of the first substrate by attraction before the first substrate is held by the upper holding unit.