This paper proposes SkeletonVR, a VR puzzle assembly application, to facilitate the education of the human skeletal system. With the use of motion-tracked controllers, the application allows users to grab and assemble bones within the virtual environment to learn about the location and orientation of the different bones within a human skeleton while also educating them on the names of the bones being interacted with. We aim to bring a new experience to users by providing an interactive and immersive environment that makes learning more intriguing while also providing different difficulty modes to keep users engaged and challenged. We further discuss students' feedback in a VR class to identify the limitations of our approach and evaluate its usefulness. While aiming at human anatomy, our interactive puzzle assembly application can be extended to other research and application domains such as chemical compound structure assembly and structure-based drug design.