A control system for an RFID-based system for assembling and verifying outbound surgical equipment corresponding to a particular surgery. A user enters a identification number of a surgery. The control system queries a database of surgery information and outputs a list of required surgical equipment, such as surgical instrument sets. An operator uses the list to pick instrument sets for loading into a shipping tote. Each set is tagged with an RFID inventory tag that stores identification information for that set such as a set name and ID number. The shipping tote is passed through an RFID reader and identification data read from the tags is compared against the identification data for sets required for that surgery. A status indicator is activated to alert a user as to whether the surgery is complete that is, all expected sets are present, or that exception handling is required. The control system updates a database such as an ERP system to reflect that the surgery including the required sets has shipped—and the sets are inventoried out to the intended recipient.