Geometrical assessments of human skulls have been conducted based on anatomical landmarks. If developed, the automatic detection of these landmarks will yield both medical and anthropological benefits. In this study, an automated system with multi-phased deep learning networks was developed to predict the three-dimensional coordinate values of craniofacial landmarks. Computed tomography images of the craniofacial area were obtained from a publicly available database. They were digitally reconstructed into three-dimensional objects. Sixteen anatomical landmarks were plotted on each of the objects, and their coordinate values were recorded. Three-phased regression deep learning networks were trained using ninety training datasets. For the evaluation, 30 testing datasets were employed. The 3D error for the first phase, which tested 30 data, was 11.60 px on average (1 px = 500/512 mm). For the second phase, it was significantly improved to 4.66 px. For the third phase, it was further significantly reduced to 2.88. This was comparable to the gaps between the landmarks, as plotted by two experienced practitioners. Our proposed method of multi-phased prediction, which conducts coarse detection first and narrows down the detection area, may be a possible solution to prediction problems, taking into account the physical limitations of memory and computation.