In intra-operative navigation, a registration procedure is performed to register the patient’s position to the pre-operative imaging data. The registration process is the main factor that determines accuracy of the navigation feedback. In this study, a novel registration protocol for craniofacial surgery is presented, that utilizes a virtual splint with marker points. The accuracy of the proposed method was evaluated by two observers in five human cadaver heads, for optical and electromagnetic navigation, and compared to maxillary bone-anchored fiducial registration (optical and electromagnetic) and surface-based registration (electromagnetic). The results showed minimal differences in accuracy compared to bone-anchored fiducials at the level of the infra-orbital rim. Both point-based techniques had lower error estimates at the infraorbital rim than surface-based registration, but surface-based registration had the lowest loss of accuracy over target distance. An advantage over existing point-based registration methods (bone-anchored fiducials, existing splint techniques) is that radiological imaging does not need to be repeated, since the need for physical fiducials to be present in the image volume is eradicated. Other advantages include reduction of invasiveness compared to bone-achnored fiducials and a possible reduction of human error in the registration process.