Due to increasing demands in the amount of content to be learned within a medical and health sciences curriculum, there are benefits towards exploring options for new and effective delivery modes. Augmented reality technology has the potential to enhance learning in physiology and anatomy, where students require a three-dimensional knowledge of human organ systems and structures. This study aimed to assess the effectiveness of learning when an identical lesson was delivered through augmented reality using either the Microsoft HoloLens or a mobile handheld tablet device. Thirty-eight pre-clinical undergraduate participants completed a lesson detailing the physiology and anatomy of the brain. Pre- and post-intervention tests were provided to evaluate acquired knowledge. After the activity, participants also completed a Likert-style questionnaire to evaluate adverse health effects experienced and assess their perceptions of the module. There were no significant differences between test scores from lesson delivery in either the HoloLens or mobile-based augmented reality. However, a significant increase was reported in dizziness when using the HoloLens (25% higher, n = 19, p = 0.04). No other adverse health effects, such as nausea, disorientation or fatigue were observed. Both modes were effective for learning, providing evidence to support educators and developers wishing to adopt an augmented reality method of delivery in health sciences and medicine.