In a substrate processing apparatus according to the present invention, wafer transfer timing with which wafers are to be transferred to individual processing chambers from a cassette container is determined in correspondence to each processing chamber, based upon the lengths of time required to process a single wafer in the processing chambers. Then, wafers are transferred from the cassette container in conformance to the transfer timing thus determined. By setting the wafer transfer timing with which wafers are transferred from the cassette container in coordination with the lengths of processing time at the individual processing chambers, the operation rates in the processing chambers are improved and ultimately, the throughput of the apparatus is improved.