A wafer bonding apparatus includes a first bonding chuck to fix a first wafer on a first surface thereof, a second bonding chuck to fix a second wafer on a second surface thereof facing the first surface, a bonding initiation member at a center of the first bonding chuck to push the first wafer towards the second surface, and a membrane member including a protrusion protruding from a center portion of the second surface towards the first surface, and a planar portion defining the protrusion on an outer region surrounding the center portion.