A substrate processing apparatus configured to dry a substrate with a processing fluid in a supercritical state includes: a processing vessel; a substrate holder configured to hold the substrate horizontally within the processing vessel; a first supply line connected to a first fluid supply provided at the processing vessel and configured to supply the processing fluid into the processing vessel; a drain line connected to a drain unit provided at the processing vessel and configured to drain the processing fluid from the processing vessel; a bypass line branched off from the first supply line and connected to the drain line, the bypass line being configured to allow at least a part of the processing fluid flowing in the first supply line to be drained into the drain line without passing through the processing vessel; and a bypass opening/closing valve configured to open or close the bypass line.