A substrate processing apparatus capable of accurately aligning a center of a substrate, such as a wafer, with an axis of a substrate stage and capable of processing the substrate without bending the substrate is disclosed. The substrate processing apparatus includes a first substrate stage having a first substrate-holding surface configured to hold a first region in a lower surface of the substrate, a second substrate stage having a second substrate-holding surface configured to hold a second region in the lower surface of the substrate, a stage elevator configured to move the first substrate-holding surface between an elevated position higher than the second substrate-holding surface and a lowered position lower than the second substrate-holding surface, and an aligner configured to measure an amount of eccentricity of a center of the substrate from the axis of the second substrate stage and align the center of the substrate with the axis of the second substrate stage.