SOKENDAI has 6 schools and 20 departments. School of Cultural and Social Studies, School of Physical Sciences, School of High Energy Accelerator Sciences, School of Multidisciplinary Sciences, and School of Life Science together hold charge of 19 departments, which are housed in 18 affiliated research institutes and operated by 4 Inter-University Research Institute Corporations and Japan Aerospace Exploration Agency.
School of Advanced Sciences, which is attached directly to SOKENDAI Headquarters and does not have a parent institute, has one department to conduct research into the evolution of life and the relationship between science and society.
In addition, the University Library, the Research Center for Integrative Evolutionary Science, the Center for Educational Development, and the Center for Academic Information Services have been established as university-wide facilities for all 6 schools.