According to one embodiment, a bonding apparatus for processing a retained substrate includes a main body unit, a nozzle, a gas supply unit, and a substrate support unit. The nozzle opens on a face of the main body unit on a side that a first substrate is retained. The gas supply unit is configured to supply gas to the nozzle, to apply suction to the first substrate and to separate the substrate from the face of the main body unit. The substrate support unit is configured to support a peripheral edge portion of a second substrate provided in opposition to the first substrate with a predetermined gap.