Augmented reality (AR), a new generation of technology, has attracted the attention of educators in recent years. In this study, a MagicBook was developed for a neuroanatomy topic by using mobile augmented reality (mAR) technology. This technology integrates virtual learning objects into the real world and allow users to interact with the environment using mobile devices. The purpose of this study was to determine the effects of learning anatomy via mAR on medical students' academic achievement and cognitive load. The mixed method was applied in the study. The random sample consisted of 70 second-year undergraduate medical students: 34 in an experimental group and 36 in a control group. Academic achievement test and cognitive load scale were used as data collection tool. A one-way MANOVA test was used for analysis. The experimental group, which used mAR applications, reported higher achievement and lower cognitive load. The use of mAR applications in anatomy education contributed to the formation of an effective and productive learning environment. Student cognitive load decreased as abstract information became concrete in printed books via multimedia materials in mAR applications. Additionally, students were able to access the materials in the MagicBook anytime and anywhere they wanted. The mobile learning approach helped students learn better by exerting less cognitive effort. Moreover, the sensory experience and real time interaction with environment may provide learning satisfaction and enable students to structure their knowledge to complete the learning tasks.