| Region | Country | City | Name | Department |
| Asia | Bangladesh | Dhaka | The Bangladesh Network office for Urban Safety (Branch Office, IIS, UT in BUET) | Institute of Industrial Science |
| Asia | China | Beijing | China-Japan Joint Laboratory | The Institute of Medical Science |
| Asia | China | Beijing | Institute of Medical Science Beijing Project Office | The Institute of Medical Science |
| Asia | China | Harbin | Joint Research Program at HVRI | The Institute of Medical Science |
| Asia | China | Nanjing | ZENSHO Nanjing Center for Liberal Arts, the University of Tokyo | Graduate School of Arts and Sciences |
| Asia | China | Shanghai | Institute for Advanced Studies on Asia Exchange Base | Institute for Advanced Studies on Asia |
| Asia | China | Yangbajing, Tibet | The Tibet ASgamma Laboratory, Institute for Cosmic Ray Research, the University of Tokyo | Institute for Cosmic Ray Research |
| Asia | India | Delhi | The University of Tokyo India Office | Research Promotion Department |
| Asia | Mongolia | Ulan Bator | Center for Biodiversity and Ecosystem Restoration in Mongolia, the University of Tokyo | Graduate School of Agricultural and Life Sciences |
| Asia | Thailand | Pathumthani | The Regional Network Office of Urban Safety (Branch Office, IIS, UT in AIT) | Institute of Industrial Science |
| Asia | Thailand | Pathumthani | Southeast Asian Center for Water Environment Technology (SACWET), the University of Tokyo | Research Center for Water Environment Technology, School of Engineering |
| Central and South America | Bolivia | Mt. Chacaltaya | Chacaltaya Observatory of Cosmic Physics, Institute for Cosmic Ray Research, the University of Tokyo | Institute for Cosmic Ray Research |
| Central and South America | Chile | San Pedro de Atacama | The University of Tokyo Atacama Observatory | Graduate School of Science |
| Europe | France | Lille | IIS/UTokyo bureau for European Collaboration (IBEC) | Institute of Industrial Science |
| Europe | France | Lille | SMMIL-E | Institute of Industrial Science |
| Europe | Italy | Milan | IFOM-IQB Joint Laboratory | Institute for Quantitative Biosciences |
| Europe | Italy | Somma Vesuviana, Naples | Research Unit for the study of roman archaeological sites in southern Italy | Graduate School of Arts and Sciences |
| Europe | Spain | Canary Islands, La Palma | High Energy Astro Physics Observatory in Canary, Institute for Cosmic Ray Research, the University of Tokyo | Institute for Cosmic Ray Research |
| Europe | Switzerland | Geneva | CERN Office for Elementary Particle Physics, the University of Tokyo | International Center for Elementary Particle Physics |
| Europe | Switzerland | Villigen | PSI Office for Elementary Particle Physics, the University of Tokyo | International Center for Elementary Particle Physics |
| North America | Canada | Toronto | North American Office, IIS, UT | Institute of Industrial Science |
| North America | USA | Boston, Massachusetts | IRCN Boston Collaborative Research Center | International Research Center for Neurointelligence |
| North America | USA | Berkeley, California | IPMU Berkeley satellite | Kavli Institute for the Physics and Mathematics of the Universe |
| North America | USA | Manoa, Hawaii | RCAST, the University of Tokyo UHM-CDS Satellite Office | Research Center for Advanced Science and Technology |
| North America | USA | New York | The University of Tokyo New York Office | External Relations Department |
| North America | USA | Oak Ridge, Tennessee | US-Japan Cooperative Program on Neutron Scattering | The Institute for Solid State Physics |
| North America | USA | Millard, Utah | Observatory for Highest Energy Cosmic Rays, Institute for Cosmic Ray Research, the University of Tokyo | Institute for Cosmic Ray Research |
