The aim of this study was to investigate the effect of immersive three-dimensional (3D) interactive virtual reality (VR) on anatomy training in undergraduate physical therapy students. A total of 72 students were included in the study. The students were randomized into control (n = 36) and VR (n = 36) group according to the Kolb Learning Style Inventory, sex, and Purdue Spatial Visualization Test Rotations (PSVT-R). Each student completed a pre-intervention and post-intervention test, consisting of 15 multiple-choice questions. There was no significant difference between the two groups in terms of age, sex, Kolb Learning Style Inventory distribution, and the PSVT-R (P > 0.05). The post-test scores were significantly higher compared to pre-test scores in both the VR group (P < 0.001) and the control group (P < 0.001). The difference between the pre-test and post-test results was found to be significantly higher in favor of the VR group (P < 0.001). In this study, anatomy training with a 3D immersive VR system was found to be beneficial. These results suggest that VR systems can be used as an alternative method to the conventional anatomy training approach for health students.