System and method for implementing integrated transportation control in a wafer fabrication facility are described. One embodiment is a factory automation system for a wafer fabrication facility (“fab”) comprising a plurality of bays, wherein each of the bays comprise a plurality of equipment interconnected by an intrabay overhead transport (“OHT”) system, and first and second interbay OHT systems each for interconnecting the intrabay OHT systems. The factory automation system comprises a manufacturing execution system (“MES”) for providing lot information regarding wafers being processed in the fab, a material control system (“MCS”) for providing traffic information regarding transportation of wafers in the fab, and an integrated transportation control (“ITC”) system for using the lot information from the MES and the traffic information from the MCS for selecting a destination and a route to the selected destination for a wafer carrier containing wafers in response to a transfer request.