A substrate processing method implemented in a substrate processing system that includes an etching apparatus that carries out plasma etching processing on a substrate and a vacuum-type substrate transferring apparatus to which the etching apparatus is connected is provided. A first step includes forming a protective film on a rear surface of the substrate before the plasma etching processing is carried out. The protective film prevents the rear surface of the substrate from being scratched by an electrostatic chuck that electrostatically attracts the substrate during the plasma etching processing. A second step includes electrostatically attracting the substrate to the electrostatic chuck such that the electrostatic chuck directly contacts the rear surface of the substrate and of carrying out the plasma etching processing on the substrate. A third step includes removing the protective film from the rear surface of the substrate after the plasma etching processing has been carried out.