Developmental dysplasia of the hip (DDH) presents a considerable surgical challenge in total hip arthroplasty (THA). Although the usefulness of computed tomography (CT)-based navigation in cup alignment has been reported, few reports have evaluated three-dimensional (3-D) cup positioning against the acetabulum specifically in patients with DDH. The purpose of this study was to evaluate the efficacy of a CT-based navigation system for alignment and spatial positioning of the cup in THA for patients with DDH. We reviewed 174 DDH THA cases in which CT-based navigation was used, and 75 cases in which a mechanical guide was used as a control group. Postoperative cup alignment and spatial positioning were evaluated by superimposition of a 3-D cup template onto the actual implanted cup using postoperative CT images, with pelvic coordinates matching the preoperative planning. The proportion within the combined target zone (inclination and anteversion) was 97.7% in the navigation group and 61.3% in the non-navigation group. The mean absolute error between the intraoperative record and the postoperative measurement was 1.5° ± 1.3° for inclination and 2.1° ± 1.8° for anteversion in the navigation group. For acetabular cup positioning, the mean discrepancy between the preoperative planning and the postoperative measurements was 1.9 ± 1.6 mm on the transverse axis, 2.8 ± 2.3 mm on the longitudinal axis, and 1.7 ± 1.3 mm on the sagittal axis. THA using a CT-based navigation system achieved quite high accuracy of cup alignment angles and spatial cup positioning in primary THA for patients with DDH.