A substrate processing apparatus performs increasing a pressure within a processing vessel up to a processing pressure higher than a threshold pressure of a processing fluid by supplying the processing fluid into the processing vessel in which a substrate having thereon a liquid is accommodated; and supplying the processing fluid into the processing vessel and draining the processing fluid while maintaining the pressure within the processing vessel at a level allowing the processing fluid to be maintained in a supercritical state. The increasing of the pressure includes: increasing the pressure to a first pressure; and increasing the pressure to the processing pressure from the first pressure. A temperature of the substrate is controlled to a first temperature in the increasing of the pressure to the first pressure, and is controlled to a second temperature higher than the first temperature in the increasing of the pressure to the processing pressure.