We conducted experimental classes in an elementary school to examine how the advantages of using stereoscopic 3D images could be applied in education. More specifically, we selected a unit of the Tumulus period in Japan for sixth-graders as the source of our 3D educational materials. This unit represents part of the coursework for the topic of Japanese history. The educational materials used in our study included stereoscopic 3D images for examining the stone chambers and Haniwa (i.e., terracotta clay figures) of the Tumulus period. The results of our experimental class showed that 3D educational materials helped students focus on specific parts in images such as attached objects of the Haniwa and also understand 3D spaces and concavo-convex shapes. The experimental class revealed that 3D educational materials also helped students come up with novel questions regarding attached objects of the Haniwa, and Haniwa's spatial balance and spatial alignment. The results suggest that the educational use of stereoscopic 3D images is worthwhile in that they lead to question and hypothesis generation and an inquiry-based learning approach to history.