We have thus far conducted a special-needs education program using e-learning for students experiencing learning difficulties in regular classrooms. The results for improving cognitive function and an attempt to investigate accompanying changes in brain function are summarized. The learning tasks for and during the education program using personal computers focused on training students in “reading” capabilities and they were designed to focus on training them to attain accuracy and fluency. The learning environment for Japanese students is currently in flux and the development of instructional materials using new technologies is an urgent issue. However, learning systems that can be used in e-learning environments are currently limited to certain conventional classroom activities and the presentation of self-study subjects, and these are not considered to produce adequate learning results. Learning systems designed for e-learning study environments such as our preliminary system will thus be indispensable in the future. In addition, we argue that it is necessary to incorporate knowledge from cognitive-science research into the implementation of such systems. We also discuss the possibility that conducting research on brain function in the process of accomplishing learning will benefit both researchers and teachers in the field.