The Graduate School of System Informatics was established in April 2010 when the Department of Computer Science and Systems Engineering was separated from the Graduate School of Engineering. Both the Master’s Program and Doctoral Program of the Graduate School of System Informatics had been organized into the following three departments: Systems Science, Information Science, and Computational Science. From April 1, 2023, the Graduate School of System Informatics was reorganized as one department: System Informatics. 

The Graduate School of System Informatics engages in research and education in the fields of systems technologies, information technologies, and computational technologies, focusing on system information (significant information that exists in a broad range of systems, including nature, engineering, and society) to create and expand new academic disciplines, in order to conceive new knowledge and values. The Graduate School hopes to train people possessing great creativity and a cosmopolitan outlook in order to contribute towards this objective. For this purpose, the Graduate School is committed to enrolling students from a wide range of backgrounds, not only from Japan but also from overseas.

The Graduate School of System Informatics offers Master and Ph.D. programs in System Informatics. Students can continue in a consistent program from Master's to the Ph.D. degree. Upon completion of the Master's Program, students receive a Master of System Informatics or Master of Engineering. Those who continue will receive a Doctor of Philosophy，Doctor of Philosophy in System Informatics, Doctor of Philosophy in Engineering, or Doctor of Philosophy in Computational Science upon completion of their program. 

The Graduate School of System Informatics has one department (Department of System Informatics) with 21 divisions and 5 collaborative divisions.