This study is a psychologically-based, practical approach that uses “visual phenomena” as a means to help develop science literacy for junior high school students. Specifically, by using “visual illusions” as the basis of our resource materials, we (i) developed a teaching method; (ii) conducted classes incorporating a visual experiment tool (experience-based education); and (iii) measured the effects of the classes (educational evaluation questionnaire). The results of this approach have shown that students developed a greater understanding of the workings of the brain and mind, while simultaneously gaining an increased interest in humans and science, through the process of experiencing the visual phenomena, by measuring about their own visual reactions, and by thinking about causal relationships. Visual phenomena, as a sensory experience, aided the students in gaining a deeper understanding of the unique characteristics of human biology through their experiences. Students also understood that scientific study is not limited to the physical world (natural sciences) but can also comprise human reactions and behavior. An additional benefit of this research is that our approach enabled us to develop a visual illusion experiment tool that can be used on the computer. By using these types of IT applications, we expect to be able to positively affect science education towards the development of science literacy in students that can be realized through increased student motivation to learn, and by providing teachers with a visual experiment tool that enables direct instruction to students.