Many application areas for augmented reality (AR) and virtual reality (VR) emerged with the technological advances. These technologies, which initially appeared in sectors such as entertainment and games, are now widely used in the field of health care. In this study, a traditional simulator named SABAS is designed with its all components to be used in the training of brain anatomy. The designed simulator is equipped with AR and VR supported innovative e-learning technologies in order to examine and learn the structure of the human brain, whose anatomical structure and functioning is complex, using 3D models in anatomy education. This smartphone-aided application is achieved a high level of success in examination of brain anatomy with the additional features such as interface design and application usability. After the cornerstones of this designed prototype application are presented, the required suggestions are obtained from experts and healthcare professionals and it is observed that the application worked with maximum efficiency. In the study, the effectiveness of the VR and AR aided SABAS mobile application simulator, developed to teach the anatomical structure of the brain, is evaluated based on the experiences of 30 participants who wanted to voluntarily participate in the study.