A substrate processing apparatus includes: a reaction tube including inner and outer tubes installed to surround the inner tube; a substrate holder for holding substrates in a vertical direction; gas nozzles installed in a gap between the outer and inner tubes and having supply holes from which a gas is supplied toward an inlet port of the inner tube; a gas supply system for feeding gases to the reaction tube though the gas nozzles; an outlet port formed in the inner tube to flow out the gas; a discharge port for discharging the gas; a discharge part for discharging the gas staying in the gap from the discharge port; and a controller for controlling the gas supply system to supply a precursor gas and an inert gas and for causing the discharge part to purge the gas staying in the gap with the inert gas.