This application relates to an automated three-dimensional (3D) cell culture system. The system includes a first body including a cell culture space in which a scaffold, on which cells are cultured, is provided and the cells are cultured thereon, and a medium storage space which is partitioned from the cell culture space by a first partition wall, in which a medium is provided and stored, and which surrounds the cell culture space, wherein the first partition wall has a drain hole to communicate the medium storage space with the cell culture space. The system also includes a communication pipe provided at the first partition wall to drain the medium of the cell culture space to the outside by a siphon action. The system further includes a second body including a medium recovery space located under the first body and recovering and externally draining the medium drained through the communication pipe.