A pharmaceutical container processor for processing pharmaceutical containers includes a set of container operation stations along which a set of container operations occur. The set of container operation stations includes a storage station where pharmaceutical containers are stored; a first identification station where pharmaceutical containers are each identified; a labeling station where a label is applied to pharmaceutical containers; a second identification station where pharmaceutical containers are each identified after the label is applied; and an outlet station where pharmaceutical containers are moved to after said pharmaceutical containers are identified at the second identification station. First and second container transporters move each pharmaceutical container through the set of container operation stations. Each pharmaceutical container is transferred from the first container transporter to the second container transporter along the set of container operation stations.