Planning a three-dimensional (3D) osteotomy using computed tomography (CT) data is useful especially in cases with complex deformities. Furthermore, CT-based navigation system allows the preoperative virtual planning to be replicated in actual surgery. However, one disadvantage when using navigation systems is that when osteotomies are performed on tracker-attached bone, the bone fragments on the side that were cut away cannot be tracked. This is especially problematic when performing multiple osteotomies on bones with complex deformities. We solved this problem by creating a 3D printed bone model that can be referenced intraoperatively and used in combination with the navigation system. We applied these techniques to perform segmental corrective osteotomy for a complex tibial deformity with intramedullary nail (IMN) fixation case of hereditary vitamin D-resistant hypophosphatemic rickets (HVDRR) in an adult man. Due to the patient’s history of multiple surgeries, the affected tibia had a narrow and partially closed medullary canal. Therefore, we planned to use an IMN for correction and fixation of tibial deformity to protect the thin and stretched skin around the deformed tibia. With the assistance of CT-based navigation, we could perform an accurate three-dimensional tibial osteotomy. Moreover, we could perform accurate preparation of closed medullary canal for the IMN placement by referring to the 3D printed bone models. Six months after the operation, the bone union at the osteotomy sites was confirmed and the patient was able to return to his normal life and work.