There is disclosed a substrate processing apparatus which can align a center of a substrate, such as a wafer, with a central axis of a substrate stage with high accuracy. The substrate processing apparatus includes: an eccentricity detector configured to obtain an amount of eccentricity and an eccentricity direction of a center of the substrate, when held on a centering stage, from a central axis of the centering stage; and an aligner configured to perform a centering operation of moving and rotating the centering stage until the center of the substrate on the centering stage is located on a central axis of a processing stage. The aligner is configured to calculate a distance by which the centering stage is to be moved and an angle through which the centering stage is to be rotated, based on an initial relative position of the central axis of the centering stage with respect to the central axis of the processing stage, the amount of eccentricity, and the eccentricity direction.