Background: Immersive VR is still rarely used as an intervention for meeting the affective end goals of student learning despite its positive impact on affection. Also, studies regarding the use of immersive VR as an intervention for affective achievement in broader educational contexts are still lacking. Objectives: This study aimed to examine the effect of immersive VR and perspective-taking on presence and empathy. Methods: A total of 148 pre-service teachers participated in experiments, using either a head-mounted display or a flat screen device to view two VR videos with different perspective-taking affordances. This study used a mixed design with one between-subject variable of immersion level and one within-subject variable of perspective-taking to explore how immersive VR experiences influenced participants' perceived level of presence and empathy. Results and Conclusions: The results showed that the level of immersion affects perceived presence, but it was the type of perspective-taking that affects empathetic reactions. We also found an interaction effect between immersion levels and perspective-taking. The direct embodiment in VR combined with high immersion produced stronger empathy than with low immersion, while the perspective of an observer was better in evoking empathy when experienced with low immersion. Implications: This study gives a guidance on how to take advantage of this new technology in educational settings, and apply it to instructional activities to enhance students' empathy. In addition, it could serve as a reference when developing or introducing educational contents with respect to the types of contents that are more effective in educational settings.