Chordomas are rare, locally malignant tumors derived from remnants of the notochord that can manifest anywhere in the spine or base of the skull. Surgical treatment for chordomas of the lumbar spine often fails to achieve successful en bloc resection, which is critical to minimizing recurrence risk. In this case report, the authors describe total en bloc resection of a lumbar vertebral body chordoma via the first documented approach of navigated ultrasonic osteotomy for spondylectomy. The patient is a 43-year old male with end-stage renal disease, requiring dialysis, secondary to diabetes mellitus. The lesion in question was incidentally discovered in the L5 vertebral body during full body scanning for evaluation for a renal transplant. The lesion was diagnosed as chordoma via percutaneous co-axial needle biopsy. Allogeneic renal transplant was canceled pending treatment of this newly discovered lesion. A combined, staged approach of L3-pelvis posterior instrumented fusion, L5 laminectomy and spondylectomy, and anterior L5 cage reconstruction with L4-S1 fusion was planned. Intraoperative CT scan was performed and stereotactic osteotomies were planned. Ultrasonic osteotome (SONOPET ® Ultrasonic Aspirator, Stryker Corporation, Kalamazoo, Michigan) was registered as a navigation tool and employed, after verification, to complete the posterior stereotactic osteotomies, with postoperative CT, MRI and pathology demonstrating successful en bloc resection. The navigated osteotome provided a critical combination of surgical precision and efficiency intraoperatively. This approach offers a promising technological adjunct for treatment of complex spine tumors requiring precise resection and reconstruction.