A substrate processing apparatus which can remove foreign matters attached to the entire upper surface of a substrate such as a wafer is disclosed. The substrate processing apparatus includes: a substrate holding apparatus; and a processing head configured to scrub an upper surface of a substrate. The substrate holding apparatus includes: a substrate holder configured to hold the substrate; and a substrate rotating mechanism configured to rotate the substrate held by the substrate holder. The substrate holder is disposed below the upper surface of the substrate so as not to project above the upper surface of the substrate in a state where the substrate is held by the substrate holder.