A substrate processing apparatus includes a plurality of placement parts on which a substrate container is placed, a driving part configured to move the plurality of placement parts, a transport mechanism configured to load the substrate container into one of the plurality of placement parts and to unload the substrate container from one of the plurality of placement parts, and a controller configured to control the driving pan and the transport mechanism so that by raising or lowering the transport mechanism while keeping a support of the transport mechanism unmoved in an initial position, the substrate container is delivered from one of the plurality of placement parts to the support of the transport mechanism, and the substrate container is delivered from the support of the transport mechanism to one of the plurality of placement parts.