Disclosed is a substrate processing apparatus including: a housing section configured to house a substrate; a transfer chamber that includes a plurality of airtight chambers connected to the periphery thereof, and a transfer mechanism provided therewithin, each of the plurality of airtight chambers being configured to process the substrate under an airtight state, and the transfer mechanism being configured to transfer the substrate to and from the airtight chambers; a carry-in section configured to carry the substrate into the transfer chamber via a first opening provided in the transfer chamber; and a carry-out section configured to carry out the substrate discharged from a second opening provided at a different position from that of the first opening of the transfer chamber, to the housing section, without returning the substrate to the transfer chamber.