There is provided a substrate processing apparatus for processing a substrate, including: a storage part provided on an uppermost portion of the substrate processing apparatus and on which a substrate accommodation container for accommodating the substrate is placed; and a first transfer device configured to directly or indirectly deliver the substrate accommodation container between the storage part and a loading/unloading part, wherein the loading/unloading part is configured to place the substrate accommodation container thereon in the substrate processing apparatus and to load and unload the substrate into and from a processing part of the substrate processing apparatus, and the first transfer device is configured to deliver the substrate accommodation container with respect to an overhead hoist transport that moves above the substrate processing apparatus.