(As of October 1st, 2025)
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| Dean | Prof. | Etsuro Hatano |
| Chairperson of Department (Human Health Science) | Prof. | Tomoki Aoyama |
| Member of University Education and Research Council | Prof. | Akifumi Takaori |
| Member of University Education and Research Council | Prof. | Yasuyuki Fujita |
| Vice-Dean | Prof. | Osamu Takeuchi |
| Vice-Dean | Prof. | Kenji Kabashima |
| Vice-Dean | Prof. | Takashi Mizowaki |
| Vice-Dean | Prof. | Yuichi Imanaka |
| Vice-Dean | Prof. | Tomoki Aoyama |
| Deputy-Dean | Prof. | Yumi Matsumura |
| Deputy-Dean | Prof. | Hirohide Takebayashi |
| Deputy-Dean | Prof. | Riki Matsumoto |
| Chairperson of Division (Medicine) | Prof. | Etsuro Hatano |
| Chairperson of Division (Medical Science) | Prof. | Kenji Kabashima |
| Chairperson of Division (School of Public Health) | Prof. | Yuichi Imanaka |
| Chairperson of Division (Human Health Science) | Prof. | Tomoki Aoyama |
| Chairperson of Division (Kyoto-McGill International Collaborative Program in Genomic Medicine) | Prof. | Mitinori Saitou |
| Director of Institute of Laboratory Animals | Prof. | Dai Watanabe |
| Director of Congenital Anomaly Research Center | Prof. | Hironori Haga |
| Director of Center for Anatomical Studies | Prof. | Hironori Haga |
| Director of Human Brain Research Center | Prof. | Takashi Hanakawa |
| Director of Center for Genomic Medicine | Prof. | Fumihiko Matsuda |
| Director of Center for Medical Education | Prof. | Etsuro Hatano |
| Director of Center for Cancer Immunotherapy and Immunobiology | Distinguished Prof. | Tasuku Honjo |
| Director of Center for digital transformation of healthcare | Prof. | Tomohiro Kuroda |
| Director of Health Security Center | Prof. | Yuichi Imanaka |
| Director of Medical Library | Prof. | Toshiya Murai |
| Director of University Hospital | Prof. | Akifumi Takaori |
| Assistant Director of University Hospital | Prof. | Shuich Matsuda |
| Assistant Director of University Hospital | Prof. | Daisuke Yabe |
| Assistant Director of University Hospital | Prof. | Hiroshi Seno |
| Assistant Director of University Hospital | Prof. | Toyohiro Hirai |
| Assistant Director of University Hospital | Prof. | Takashi Mizowaki |