On a spectrum from fully real to fully virtual environments, augmented reality (AR) systems allow a user to visualize three-dimensional objects. AR combines elements of real and virtual environments allowing the user to maintain a sense of presence in the real environment while manipulating virtual objects. Virtual reality (VR) immerses the user into a virtual environment, typically through the use of a head-mounted display (HMD). As consumer access to AR/VR has increased over the past few years, so have the potential applications for these systems to enhance training and education. Anatomy is one such field that requires a thorough understanding of difficult, spatial relationships, and serves as the knowledge foundation for medical practitioners. Some work has been done with newer AR or VR systems for anatomical training, but a comparison between the two systems for (i) anatomical knowledge acquisition, and (ii) the workload incurred by the learner is lacking. The present work provides a comparison between AR (i.e., zSpace) and VR (i.e., HTC Vive) for the learning of macroscopic brain anatomy. A suite of objective (pre/post-learning tests), subjective (surveys), and physiological (EEG) measures were used to provide a comprehensive evaluation of AR and VR systems for anatomical training. Results suggest a high degree of similarity between AR and VR, yet hint at some differences in the associated cognitive processes. These results inform selection of the most beneficial training platform for anatomical knowledge acquisition in first-time learners and provide insight into alternative implementations for these emerging technologies.