A substrate processing apparatus includes a processing liquid supply nozzle to supply a processing liquid to a substrate, a storage portion that stores the processing liquid supplied, a liquid-sending pipe that sends the processing liquid stored in the storage portion to the nozzle, a flow pipe that allows a processing liquid to flow therethrough, an oxygen concentration meter interposed in the flow pipe, a hypoxic fluid supply pipe that is in communication with the flow pipe and that sends a hypoxic fluid to the flow pipe, and a flow rate changing valve interposed in the hypoxic fluid supply pipe. A flow-rate-changing controller controls the flow rate changing valve so that the hypoxic fluid is supplied to the flow pipe until an inside of the flow pipe is filled with the hypoxic fluid when the processing liquid inside the flow pipe is drained.