There is provided a substrate processing apparatus including: a substrate holder configured to hold a substrate on which a resist pattern is formed; a rinse solution supply unit configured to supply a rinse solution onto the substrate held by the substrate holder; a vapor supply unit configured to supply vapor of a first processing solution, which hydrophobicizes the resist pattern, onto the substrate on which the rinse solution is supplied from the rinse solution supply unit; and a rinse solution removing unit configured to remove the rinse solution from the substrate in an atmosphere including the vapor of the first processing solution supplied from the vapor supply unit.