Intraoperative navigation is a helpful tool in complex anatomical regions or procedures. The mobility of the mandible in relation to the skull base limits the use of navigation tools on the lower jaw if the reference device is installed on the forehead. A new workflow that allows navigation-assisted sagittal split osteotomy in orthognathic surgery using a separate non-invasive mandibular registration technique has been developed. An evaluation of accuracy in different anatomical regions and with different registration techniques was performed on skull models and skulls with movable mandibles. The mean inaccuracy was 1.51mm, with no significant difference between anatomical sites. Using a splint-based reference device allows the movable mandible to be registered independently from the midface. Registration using metal points in the splint provides higher accuracy than using interdental anatomical landmarks. The workflow could be transferred successfully to patient treatment. Navigation-assisted osteotomy by Obwegeser-Dal Pont technique was performed without any complication in six patients. The mean deviation from the planned osteotomy line was 1.52mm. The navigated sagittal split ramus osteotomy seems to be a suitable technique to increase patient safety.