A system and method for cleaning boxes used for handling flat media includes a rotor rotatably mounted within an enclosure, with spray nozzles in the enclosure for spraying fluid toward the rotor. The rotor has at least one box holder assembly for holding a box. At least one retainer bar is located on the rotor for engaging a front section of the box to retain the box in the box holder assembly during rotation of the rotor. The retainer bar is preferably moveable from a first position where the retainer bar restrains the box on the box holder assembly, to a second position where the retainer bar is moved away from the box. The box holder assembly may alternatively include a base with a plurality of grooved elements thereon that are adapted to engage a flange on the box for securing the box to the box holder assembly.