A method of processing a substrate includes loading the substrate to which a processing liquid is adhered, inside a processing container, removing the processing liquid adhering to the substrate by supplying a first organic solvent to the loaded substrate, causing the substrate to be water-repellent by supplying a water repellent to the substrate from which the processing liquid has been removed, supplying a second organic solvent to the water-repellent substrate, and drying the substrate by volatilizing the second organic solvent adhering to the substrate.