A pellet magazine includes a plurality of pellet bores sized to receive pellets for loading into a fuel rod. A fuel rod loading system includes a plurality of pellet loading stations each designated to load a single pellet type into one or more pellet bores of the pellet magazine, a rod loading station configured to unload pellets from the pellet bores of the pellet magazine into a fuel rod, and a conveyance system configured to transport the pellet magazine to the loading stations and then to the rod loading station in a defined sequence.