In this study, a new approach to the implementation of Augmented Reality (AR) in the educational environment was taken by creating a Chemistry Augmented Reality Learning System (CARLS), using the existing teaching curriculum, together with physical activity. This system combined learning with three types of physical activity: aerobic fitness, muscle strength and flexibility fitness. This study reveals that the students using all three types of physical activity together with CARLS result in significantly higher academic performance compared to the traditional Keyboard-Mouse CAI (KMCAI). This improvement is most evident for the non-memorized knowledge component of Science. Moreover, the students in the AR group with 'muscle strength' physical activity had significantly more positive learning attitude change toward Science than those in the KMCAI group. A great additional benefit of our approach is that, students also obtained more physical fitness while learning.