The primary treatment for patients with sacral chordoma is en bloc surgical resection with negative margins, which has been shown to reduce local recurrence and tumor-related morbidity. Here we describe the use of intraoperative neuronavigation using preoperative spine magnetic resonance imaging fused to intraoperative computed tomography (CT) to create 3-dimensional tumor reconstructions in the operating room for intraoperative identification of bone and soft-tissue margins for maximal safe tumor resection. A single-institution retrospective chart review was completed to encompass our experience of 6 consecutive patients who had sacral chordoma resections using our described navigation protocol. We collected data on patient demographics, previous surgeries, radiation therapy, preoperative examination, spinal levels involved, dural involvement, estimated blood loss, surgery time, tissue diagnosis, follow-up, postoperative examination, complications, and recurrence. Primary outcome was en bloc resection with negative margins as planned preoperatively. Negative surgical margins were achieved in 5 of 5 patients, who were preoperatively planned for en bloc resection with negative margins. The most common levels involved were S4-S5. All patients had a stable or improved neurologic examination after en bloc surgical resection. The average follow-up was 5.4 months ± 84.6 days. No patient had residual or recurrent tumor at last follow-up. Magnetic resonance imaging-CT fusion and 3-dimensional reconstruction techniques using an intraoperative CT scanner with image-guided navigation to aid preoperative planning and surgical resection of sacral chordomas are not well represented in the literature. This technique can be used for planning en bloc surgical resections and for more precisely identifying tumor margins intraoperatively.