A wafer bonding apparatus including: a lower chuck to which a lower wafer is secured at a peripheral portion of the lower chuck; an upper chuck to which an upper wafer is secured; a bonding initiator for pressuring a central portion of the upper wafer until the central portion of the upper wafer reaches a central portion of the lower wafer, thereby initiating a bonding process of the upper and the lower wafers by deforming the upper wafer; and a bonding controller for controlling a bonding speed between a peripheral portion of the upper wafer and a peripheral portion of the lower wafer such that the upper wafer becomes un-deformed prior to bonding the peripheral portion of the upper wafer and the peripheral portion of the lower wafer.