The Department of Electronics and Applied Physics belongs to the Interdisciplinary Graduate School of Science and Engineering, one of five graduate schools in the Tokyo Institute of Technology. Established in 1975, the Interdisciplinary Graduate School of Science and Engineering was Japan's first independent graduate school without an undergraduate division. It is dedicated to education and research in new areas that transcend traditional frameworks.

At present, the Interdisciplinary Graduate School of Science and Engineering contains 11 departments. The school is made up of interdisciplinary departments, which are based on the philosophy of developing new interdisciplinary fields in the border areas that span several academic disciplines, and creativity-based departments, which place emphasis on creativity in new scholarly fields and on the doctoral program. The Department of Electronics and Applied Physics is one the interdisciplinary departments and was established in 2005 after the former Department of Information Processing and Advanced Applied Electronics were reorganized.

The department has a variety of programs. They are organizationally divided into three broad categories. Core chairs are made up of professors with positions in the Interdisciplinary Graduate School of Science and Engineering, external collaborative chairs are comprised of visiting professors, and joint programs are composed of professors belonging to research labs and centers on the Suzukake-dai campus. However, there is no difference in the chairs in terms of student education and research.

From the time they matriculate, students belong to the research labs of the professors who manage these chairs. They acquire credits from taking classes and receive direction on research projects. Students graduating from the department are either awarded Master's degrees (in engineering, physical science or science) or doctoral degrees (in engineering, physical science or science).