Embryology and histology are subjects that are viewed as particularly challenging by students in higher education. This negative perception is the result of many factors such as restricted access to lab facilities, lack of allocated time to these labs, and the complexity of the subject itself. One main factor that influences this viewpoint is the difficulty of grasping 3D orientation of sectioned tissues, especially regarding embryology. Attempts have been made previously to create alternative teaching methods to help alleviate these issues, but few have explored 3D visualisation. We aimed to address these issues by creating 3D embryological reconstructions from serial histology sections of a sheep embryo. These were deployed in a mobile application that allowed the user to explore the original sections in sequence, alongside the counterpart 3D model. The application was tested against a currently available eHistology programme on a cohort of life sciences graduates (n = 14) through qualitative surveys and quantitative testing through labelling and orientation-based tests. The results suggest that using a 3D modality such as the one described here significantly improves student comprehension of orientation of slides compared to current methods (p = 0.042). Furthermore, the developed application was deemed more interesting, useful, and usable than current eHistology tools (p < 0.05). Modalities such as that developed here could therefore provide a more effective approach to learning these challenging subjects potentially increasing student engagement with embryology and histology.