- International Research Unit of Integrated Complex System Science
- Unit of Computational Science
- Nano Technology Hub
- Center for Japan-Egypt Cooperation in Education and Research
- Unit for Advanced Study of Mind
- Education and Research Unit for Regional Alliances
- Research Unit for Physiological Chemistry
- Resilience Research Unit
- Unit for Science and Technology in Public Sphere
- Inter-Graduate School Unit for Sustainable Development and Survivable
- Educational Unit for Studies on Connectivity of Hills, Humans and Oceans [CoHHO]
- Elements Strategy Initiative for Catalysts and Batteries
- Elements Strategy Initiative for Structural Materials
- Research and Educational Unit of Leaders for Integrated Medical System (LIMS)
- Unit of Design
- Kyoto University Asian Studies Unit (KUASU)
- Educational Unit for Human Security Development
- Unit for Advanced Informatics Education and Education Informatization
- Unit of Synergetic Studies for Space
- Integrated Area Studies Unit
- Primatology and Wildlife Science Unit
- Future Earth Research Unit
- Tropical Research & Education Unit
- Interdisciplinary Unit for African Studies
- Unit for Himalayan Studies
- Interdisciplinary Unit for Global Health
- The Last 5X innovation R&D Center for a Smart,Happy, and Resilient Society
- The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX)
- Asian Platform for Global Sustainability & Transcultural Studies
- Chemistry and Chemical Engineering Unit for the Top Global Course
- Top Global University Project "Japan Gateway Program" Mathematics Unit