The Graduate University for Advanced Studies, founded in October 1988, was the 96th national university in Japan. Known as SOKENDAI, it is the first university to exclusively offer doctoral programs in Japan. Generally, universities and departments are named after the places where they are located or their fields of study. Differing from such traditions, SOKENDAI uses some symbolic names to express its policy, such as "the Graduate University for Advanced Studies" or "School of Advanced Sciences."

SOKENDAI is unique in concept in the world as a university affiliated with research institutes and museums administered by the Ministry of Education, Culture, Sports, Science and Technology (called Inter-University Research Institutes, or IURIs). Most professors and students work on their research and study as members of IURIs. The IURIs (also called parent institutes) support the best researchers and the finest facilities in the nation. SOKENDAI aims to apply such privileged academic environments not only to research (creation of new science and technology) but also education (fostering researchers).

SOKENDAI has no special facility in the IURIs. Instead, academic staff members including professors of SOKENDAI (sometimes concurrently) belong and work there. Thus, students, mentored at SOKENDAI both by faculty of SOKENDAI and of the IURIs, can do their research and study using the most advanced large research systems, including data, resources, manuscripts, artifacts, and archives unavailable to other scholars.