A stage control apparatus for controlling a stage on which a substrate can be placed and moved generates a target value relating to a vertical direction of the stage based upon substrate surface position information that corresponds to unevenness of the surface of the substrate and generates a drive command signal of the stage based upon a deviation signal between the target value generated and a measured position of the stage. A target frequency is decided upon a spatial frequency possessed by the unevenness of the substrate surface. In order to generate the drive command signal, use is made of a signal obtained by amplifying a component of the target frequency of the deviation signal.