Virtual presence describes a users’ perception of a virtual reality (VR) environment (VRE), specifically, of their involvement (sense of control within a virtual environment with minimal distractions) and immersion (multi-input sensory engagement providing apparent realism of objects and interactions). In education, virtual presence is a significant construct as highly immersive VREs have been linked to users reporting memorable and exciting teaching experiences. Prior research has described that adults and children report different levels of presence when subjected to identical VREs, suggesting cognition may play some role in users’ perceptions of presence. According to Piaget, concrete operational development is a watershed moment when adolescents develop the ability to understand abstract concepts and make assessments what is and is not reality. This period in cognitive development may influence children’s and adolescents’ perceptions of presence. This is an exploratory study of seventy-five 6th-grade and seventy-six 9th-grade students who participated in an instructional module about cardiac anatomy and physiology using a 3-D, haptic-enabled, VR technology. When surveyed on their perceptions of virtual presence, there were no reported differences between grade levels. When assessed using a Piagetian inventory of cognitive development, the analyses indicated that the sixth-grade students’ understanding of spatial rotation and angular geometry was positively correlated with the reported perceived control and negatively correlated with distraction. This study suggests that the spatial acuity of younger learners plays an important role when using VR technologies for science learning. This research raises questions about the relevance of users’ cognitive development when using emergent VR technologies in the K–12 science classroom.