A substarate processing apparatus capable of reducing the capacity of a space in an internal chamber. The internal chamber is housed in a space in an external chamber. A gas supply unit supplies a process gas into the space in the internal chamber. The space in the external chamber is under a reduced pressure or filled with an inert gas. An enclosure being movable and included in the internal chamber defines the space in the internal chamber with a stage heater included in the internal chamber. When a wafer is transferred in and out by a transfer arm used to transfer the wafer, the enclosure exits out of a motion range within which the transfer arm can move.