Augmented reality (AR) promises to be a valuable tool for anatomical education since any given anatomical site can be studied dynamically in three dimensions (3D). Yet, it has not been used with case-based learning in medical education despite the latter's demonstrated benefits. This research, thus, investigates the potential benefit of 3D holographic animated surgeries on functional anatomical knowledge acquisition. We developed four educational AR applications comparing two cases with and without the presence of a surgical animation. Based on this, a randomized crossover trial was conducted among second year medicine students. All subjects (n = 10) underwent a spatial visualization assessment, followed by a learning session and an anatomical knowledge test for both patient cases. The presence of a surgical animation did not lead to a significant difference in anatomical test scores. In addition, no correlation (τ = -0.092, p = 0.78) was detected between the effect of surgical animations and spatial visualization abilities. However, these results are based on non-parametric statistics, as normality could not be assumed. Further research with samples representative for the population, conducting both qualitative and quantitative analysis using verified outcome measures and parametric statistics is required to draw accurate conclusions.