A substrate transfer controlling apparatus can easily maximize throughput of a substrate processing apparatus such as a semiconductor fabrication apparatus, and can satisfy a demand for immediacy of actions of a transfer device. The substrate transfer controlling apparatus includes an input device for inputting times required for actions of transfer devices and times required to process substrates in processing devices, and a schedule calculator for calculating execution times of actions of the transfer devices for allowing a time when a final one of the substrates to be processed is fully processed and returned from the substrate processing apparatus to be earliest, based on a predetermined conditional formula including, as parameters, the inputted times. The substrate transfer controlling apparatus further includes an action commander for instructing corresponding transfer devices to perform actions at calculated execution times of the actions of the transfer devices.