Provided is a substrate processing apparatus including a substrate container transfer device configured to transfer a substrate container accommodating a substrate and purge an inside of the substrate container; a purge gas supply unit installed at the substrate container transfer device and configured to supply a purge gas into the substrate container; a substrate container standby unit configured to accommodate the substrate container; a contact preventing unit installed at the substrate container standby unit and configured to prevent a contact between the purge gas supply unit and the substrate container standby unit when the substrate container is transferred to the substrate container standby unit by the substrate container transfer device; and a control unit configured to control the substrate container transfer device and the purge gas supply unit.