Learning the basics of human anatomy is challenging for schoolchildren due to its three-dimensional nature and complexity as a system. This study created educational materials for learning about and teaching the human circulatory system based on augmented reality (AR) technology and a structure-behavior-function (SBF) model, including 2D/3D animations, a game, and a video to complement the current 2D representations in school textbooks. To evaluate the effectiveness of the materials developed, an instructional activity was carried out among fifty-one seventh- and eighth-grade students from a school in central Slovenia. A pretest, posttest, and delayed posttest for the instructional activity tested students' knowledge, and their acceptance of the AR technology was explored through a questionnaire. The results showed significant improvements in students' understanding of the basic anatomy and physiology of the human heart and circulatory system and the effects of adrenaline on the human circulatory system. Students expressed moderate enthusiasm for AR technology, showing the greatest level of acceptance of AR technology making learning more interesting and fun, improving learning, and making it easy to use. Although students showing more knowledge on the pretest expressed higher acceptance of AR technology, the gain in knowledge after an instructional activity was equally beneficial for all participants. The study indicates a beneficial effect of applying 3D animation, videos, and AR technology to understand dynamic and complex biological phenomena.