Anatomy teachers urge students to come to education sessions at the dissection rooms as well-prepared as possible. To effectuate optimal preparation, assignments are designed to guide the students’ learning processes. These assignment often include the use of anatomical figures in atlases. The role of augmented reality (AR) applications in helping students prepare for body donor-based teaching sessions at the dissection rooms remains quite elusive. Therefore, this study examines the effects of the use of an AR application compared to the use of anatomical atlases in helping students (n = 28) prepare for a neuroanatomy session at the dissection rooms with prosections. The study shows that students from both groups showed a similar improvement in anatomy test scores. The amount of experienced cognitive engagement, however, is higher in the experimental AR group. Based on these results, it can be suggested that an AR application is a valid method to help students prepare and could be an alternative to the use of anatomical atlases. Nevertheless, future studies should re-investigate this research question in larger cohorts. Also, it remains unknown whether cognitive engaged students are indeed the students who are better prepared for educational sessions at the dissection rooms.