A substrate processing apparatus includes an indexer block and a processing block adjacent to the indexer block in a lateral direction of the indexer block. A plurality of processing block layers are stacked in an up-down direction in the processing block. The indexer block includes a container holding portion and a first transfer robot that transfers a substrate between the substrate container held by the container holding portion and the processing block. Each of the processing block layers includes a plurality of processing units, a substrate placing portion, a dummy-substrate housing portion, and a second transfer robot that transfers a substrate between the substrate placing portion and the plurality of processing units and that transfers a dummy substrate between the dummy-substrate housing portion and the plurality of processing units.