An automated medication preparation system for delivering a dosage of medication to a drug delivery bag having a fill port through which the medication is delivered into the bag includes an automated transport device for controllably delivering each drug delivery bag from one location to another location via a driven member. The system has a carrier that releasably captures and holds a portion of the bag and orients each bag such that the fill port of each bag is positioned at a uniform location relative to the carrier. The carrier is coupled to the transport device such that movement of the driven member is translated into movement of the carrier and the captured drug delivery bag. An automated drug delivery device is part of the system and includes a drug delivery member that sealingly mates with the fill port for delivering the dosage of medication to the bag. A controller is in communication with the automated transport device for moving the automated transport device in an indexed manner, including moving the carrier to a fill location where the fill port and the drug delivery member are aligned to permit the sealed mating between the two and transfer of the dosage of medication.