A medicine supply system including a cart supply line (48) on which a plurality of carts (8) are disposed and aligned; a first transport unit for transporting the plurality of carts (8) on the cart supply line (48); a tray discharge unit (2) for storing the trays (7) in the plurality of carts; a second transport unit for transporting the plurality of carts with the trays stored in the tray discharge unit; a cart discharge line (49) on which the plurality of carts transported by the second transport unit are aligned; a tray supply lifter (1) for supplying the trays; a tray transport line (3) for transporting the trays supplied by the tray supply lifter to the tray discharge unit; a medicine dispensing unit (4) for dispensing the medicine to the trays, and a control unit (10) for supplying the trays from the tray supplying lifter 1 based on prescription data, dispensing the medicine into the trays, transporting the trays to the tray discharge unit, and storing the trays into the carts.