The present invention provides a hydrophobicizing apparatus, hydrophobicizing method and storage medium having high vaporization efficiency of medicine liquid, capable of supplying hydrophobicizing gas with high density, and further capable of inhibiting deterioration of medicine liquid. The hydrophobicizing apparatus includes a vaporizing surface forming member of which surface is located in a vaporizing room; a vaporizing surface heating unit that heats the vaporizing surface forming member; a liquid chemical supply port that supplies a liquid chemical for a hydrophobicizing process on the surface of the vaporizing surface forming member; a gas inlet port that introduces a carrier gas into the vaporizing room; an outlet port that supplies a hydrophobicizing gas vaporized in the vaporizing room; and a processing chamber that performs the hydrophobicizing process on a substrate accommodated therein by the hydrophobicizing gas supplied through the outlet port. With this configuration, the hydrophobicizing gas of a high concentration can be supplied onto the substrate. Further, since the stored liquid chemical is not in contact with the carrier gas when a process is not being performed, degradation of the liquid chemical is suppressed.