Computer-assisted navigation plays an important role in modern craniomaxillofacial surgery. Although headpins and skull posts are widely used for the fixation of the reference frame, they require the use of invasive procedures. Headbands are easily displaced intraoperatively, thus reducing the accuracy of the surgical outcome. This study reported the utility of a novel splint integrated with a reference frame and registration markers for maxillary navigation surgery. A maxillary splint with a 10 cm resin handle was fabricated before surgery, to fix the reference frame to the splint. The splint was set after the incorporation of fiducial gutta-percha markers into both the splint and resin handle for marker-based pair-point registration. A computed tomography (CT) scan was acquired for preoperative CT-based planning. A marker-based pair-point registration procedure can be completed easily and noninvasively using this custom-made integrated splint, and maxillary navigation surgery can be performed with high accuracy. This method also provides maximum convenience for the surgeon, as the splint does not require reregistration, and can be removed temporarily when required. The splint-to-CT data registration strategy has potential applicability not only for maxillary surgery but also for otolaryngologic surgery, neurosurgery, and surgical repair after craniofacial trauma.