Background: Realistic, portable, and scalable lectures, cadaveric models, 2D atlases and computer simulations are being combined more frequently for teaching anatomy, which result in major increases in user satisfaction. However, although digital simulations may be more portable, interesting, or motivating than traditional teaching tools, whether they are superior in terms of student learning remain unclear. This paper presents a study in which the educational effectiveness of a virtual reality (VR) skull model is compared with that of cadaveric skulls and atlases. The aim of this study was to compare the results of teaching with VR to results of teaching with traditional teaching methods by administering objective questionnaires and perception surveys. Methods: A mixed-methods study with 73 medical students was conducted with three different groups, namely, the VR group (N=25), cadaver group (N=25) and atlas group (N=23). Anatomical structures were taught through an introductory lecture and model-based learning. All students completed the pre- and post-intervention tests, which comprised a theory test and an identification test. The theory test consisted of 18 multiple-choice questions, and the identification test consisted of 25 fill-in-the-blank questions. Results: The participants in all three groups had significantly higher total scores on the post-intervention test than on the pre-intervention test; the post-intervention test score in the VR group was not statistically significantly higher than the post-intervention test score of the other groups (VR: 30 [IQR: 22-33.5], cadaver: 26 [IQR: 20-31.5], atlas: 28[IQR: 20-33]; p>0.05). The participants in the VR and cadaver groups provided more positive feedback on their learning models than the atlas group (VR: 26 [IQR: 19-30], cadaver: 25 [IQR: 19.5-29.5], atlas: 12 [IQR: 9-20]; p<0.001). Conclusions: The skull virtual learning resource (VLR) was equally efficient as the cadaver skull and atlas in teaching anatomy structures. Such a model can aid individuals in understanding complex anatomical structures with a higher level of motivation and tolerable adverse effects.