Systems and methods for processing surgical instrument tray shipping totes. A control system is adapted to control a bar code reader module, an RFID module, a database module and an interface module. The control system provides functionality adapted to process incoming and outgoing surgical instrument shipping totes containing one or more RFID-enabled surgical instrument trays. A database, ERP system or other system in communication with the control system alerts the operator of the status of an incoming tote and/or trays contained in the tote to increase processing efficiency and speed.