Augmented Reality (AR) is a technology that augments reality with two- or three-dimensional computer-generated imagery (CGI), objects, or information, and allows users to interact efficiently. The aim of this study was to measure the effectiveness of Augmented Reality (AR) application in teaching Human Body anatomy and determine the attention and confidence level which contributes to learning motivation among sports school students before and after using a particular AR application online, hybrid and face to face teaching. This pre-post experimental study conducted among 32 sports school students in Bukit Jalil Sports School who registered for human anatomy subject. A written test was conducted on the topic of human body anatomy after teaching using the traditional method. Then the same group of pupils learned human body anatomy using Augmented Reality application. A post-test was conducted to evaluate the understanding and achievement. The pair sample t-test was used to determine the effectiveness between both methods. The subjects also answered a five scale Likert questionnaire to determine the attention, confidence and motivation level in learning through AR application. The paired sample t-test showed significant differences between pre- and post-test, with t(31) = −7.44, p = 0.00 (p < 0.05). This showed that learning through the Augmented Reality application is much easier and more efficient compared to the traditional method using textbooks, pictures, and diagrams. The descriptive analysis showed the mean score of attention (4.31), confidence (3.98) and motivation (4.13) are high. Results demonstrated positive significant correlation between the mean score of attention (r = 0.75), and confidence (r = 0.73) toward motivation (r = 0.84) (p < 0.001). These findings showed high levels of attention, self-confidence, and motivation among sports school students while learning using augmented reality compared to learning through the traditional method. In conclusion this study proved that AR application can increase motivation in the learning process and enhance academic performance in Human Anatomy and also other subjects.