Disclosed are a substrate processing apparatus, a substrate processing method, and a storage medium, which can process a normal substrate according to a normal schedule in parallel with a substrate to be processed in preference to other substrates. Processing block performs the same types of processes for substrates, carried therein from FOUP placing unit, by using process arms. When a priority substrate having a priority over other substrates are carried, control unit carries and processes the priority substrate in priority processing unit that can receive a next substrate among priority processing units to which a plurality of processing units are partially or wholly assigned, in preference to other substrates.