| 1897 | 6 | The Kyoto Imperial University was founded. |
| 1899 | 9 | The College of Medicine opened and the School of Medicine was established (Anatomy, Physiology, Medical Chemistry, Hygieiology, Internal Medicine (two departments), Surgical Medicine (two departments)). |
| 12 | The University Hospital opened and the Nursing School was established. | |
| 1900 | 3 | Four departments were established (Anatomy (2nd), Pathology, Pathologic Anatomy, Pharmacognosy). |
| 1901 | 6 | Two departments were established (Obstetrics and Gynecology, Ophthalmology). |
| 1902 | 5 | Four departments were established (Pediatrics, Legal Medicine, Psychiatric Medicine, Dermatology and Mycotoxicosis). |
| 1903 | 4 | The Fukuoka College of Medicine was opened and the College of Medicine was renamed The Kyoto College of Medicine. |
| 11 | The first graduation ceremony was held in the Kyoto College of Medicine. | |
| 1905 | 3 | The Department of Otorhinolaryngology was established. |
| 1906 | 4 | Two Departments were established (Orthopaedic Surgeons, Anatomy (3rd)). |
| 1909 | 5 | The Department of Internal Medicine (3rd) was established. |
| 1911 | 4 | The Fukuoka College of Medicine was separated from Kyoto Imperial University, so the Kyoto College of Medicine was renamed The College of Medicine. |
| 10 | Midwife School was established in the University Hospital. | |
| 1912 | 5 | The Department of Hygieiology (2nd) was established. |
| 1916 | 9 | The Department of Microbiology was established. |
| 1919 | 2 | The Imperial University Law was enacted and The College of Medicine was renamed Faculty of Medicine. |
| 1920 | 8 | The Department of Pharmacognosy (2nd) was established. |
| 1923 | 4 | Special Laboratory of Leprosy was established in The University Hospital. |
| 1934 | 7 | The Department of Urology was established. |
| 1938 | 6 | Special Laboratory of Leprosy was renamed Special Laboratory of Dermatology. |
| 1939 | 3 | Two departments were established (Chemistry of Drug Assay and Pharmaceutical Technochemistry). |
| 4 | The School of Pharmacy was established in the Faculty of Medicine. | |
| 1939 | 5 | The Provisional Special Division of Medicine was established. |
| 1940 | 6 | The Department of Organic Pharmaceutical Chemistry was established in the School of Pharmacy. |
| 12 | The Department of Inorganic Pharmaceutical Chemistry was established in the School of Pharmacy. | |
| 1941 | 4 | The Department of Pharmacognosy was established in the School of Pharmacy. |
| 1943 | 5 | Dentistry was established in the University Hospital. |
| 1944 | 3 | The Provisional Special Division of Medicine was renamed the Special Division of Medicine. |
| 5 | The Department of Aeromedicine was established. | |
| 8 | The Department of Physiotherapy was established. | |
| 1945 | 4 | The School of Nursing was established in the University Hospital. |
| 5 | The Department of Pharmacognosy was renamed the Department of Pharmacology. | |
| 1946 | 1 | The Department of Aeromedicine closed. The provisional Department of Environment Medicine was established in the School of Medicine. |
| 3 | The provisional Department of Environment Medicine was closed. | |
| 1947 | 9 | Kyoto Imperial University was renamed Kyoto University. |
| 1948 | 5 | The Department of the School of Nursing was established. |
| 1949 | 1 | The Department of Community Hygiene was established in the School of Medicine. |
| 5 | Kyoto University was reorganized under the new educational system of the National School Establishment Law. The Department of Physiotherapy was renamed the Department of Radiotherapeutics. The Dental Examination Clinic was moved to the Department of Oral and Maxillofacial Surgeons. | |
| 1951 | 3 | The Department of the School of Nursing was renamed the School of Nursing. |
| 4 | The Faculty of Medicine Kyoto University under the new educational system was opened. The Department of Pharmaceutics was established in the School of Pharmacy. | |
| 1952 | 3 | The provisional Department of The Special Division of Medicine was closed |
| 4 | The Department of Chemistry of Biological Medicals was established in the School of Pharmacy. | |
| 9 | The Midwife Course was established in the School of Nursing. | |
| 1953 | 4 | The Midwife School in the University Hospital was closed. |
| 1954 | 3 | The last graduation ceremony of The College of Medicine under the old system of education was held. |
| 4 | The Midwife Course of the School of Nursing was renamed the Midwife School of the Faculty of Medicine. | |
| 1955 | 4 | The Premedical Course was established. |
| 7 | Kyoto University Graduate School of Medicine was established (Physiology, Pathology, Social Medicine, Internal Medicine, Surgical Medicine). | |
| 1957 | 4 | Kyoto University Pure Line Animal Species Center was opened. Special Laboratory of Dermatology was renamed Special Research Facilities of Dermatology. |
| 1960 | 4 | In accordance with establishing the Faculty of Pharmaceutical Sciences, the School of Pharmacy (seven department) was closed. |
| 1961 | 4 | Two departments were established (Medical Chemistry (2nd), Basic Radiotherapeutics). |
| 1964 | 4 | The Department of Neurological Surgeons Sciences was established. |
| 1967 | 4 | The Department of Geriatric Gerontology was established. |
| 6 | Research Facilities of Neurology was established. | |
| 1972 | 4 | The School of Clinical Technologist was established. |
| 5 | The Institute of Laboratory Animals was established. | |
| 1973 | 3 | The School of Health Laboratory Technician was closed. |
| 4 | The Institute of Laboratory of Metabolism was established. | |
| 1974 | 4 | The Department of Biomedical Materials was established. |
| 1975 | 4 | The Midwife School was closed. The Congenital Anomaly Research Center was established. |
| 1976 | 4 | The Department of Nuclear Medicine was established. |
| 1977 | 4 | The Institute of Laboratory of Metabolism was renamed the Institute of Laboratory Immunology. The School of Nursing was closed. |
| 1978 | 4 | The School of Clinical Technology was closed. |
| 1979 | 4 | The Department of Neural Internal Medicine was established. The Center for Anatomical Studies was established. |
| 1980 | 3 | The Department of Biomedical Materials was closed. |
| 1981 | 4 | The Department of Cardiology was established. |
| 1984 | 4 | The Department of Laboratory Medicine was established. |
| 1985 | 3 | Special Research Facilities of Dermatology was closed. |
| 4 | The Department of Molecular Medicine was established in the Graduate School of Medicine (Molecular Oncology, Molecular Genetics, Molecular Disease Therapy). | |
| 1987 | 5 | The Department of Plastic Surgery was established. |
| 1990 | 6 | The Department of Brain Control Medicine was established in the Graduate School of Medicine (Morphological Brain Science, Integrative Brain Science, Brain Pathophysiology) then the Department of Anatomy (two departments) and Research Facilities of Neurology closed. |
| 1992 | 4 | The Department of Clinical Metabolism Nutrition was established. |
| 1993 | 4 | Three departments in the Graduate School of Medicine were reorganized. The Department of Physiology (Biological Sciences, Anatomical Sciences, Bioregulation), the Department of Pathology (Pathology and Tumor Biology, Basic Pathologic Condition Sciences, Contagion and Immunity Sciences), and the Department of Social Medicine (International Regional Environment Medicine, Social Preventive Services). The department of State-of-the-art and International Medicine (by Visiting Professors) was established. The Research Facilities of Immunology closed. |
| 1994 | 6 | Two departments in Graduate School of Medicine were reorganized. The Department of Internal Medicine (Clinical Pathologic Condition Medicine, Clinical Pathologic Organocondition Medicine, Medical Control), and the Department of Molecular Medicine (Molecular and Cellular Biology, Medical Genetics). |
| 1995 | 4 | Two departments in the Graduate School of Medicine were reorganized. The Department of Surgical Medicine (Transplant Immunology, Organ Surgical Medicine, Sensory Pathologic Condition Sciences), and the Department of Brain Control Medicine (Morphological Brain Science, Brain Pathophysiology) |
| 1997 | 4 | The Department of State-of-the-art and International Medicine (by Visiting Professors) was opened as a cooperative graduate school. |
| 1998 | 4 | Three facilities of the Faculty of Medicine were attached to the Graduate School of Medicine. In accordance with reorganizing the Institute for Chest Diseases Research, three departments of the institute were merged with the Departments of the Graduate School of Medicine, and the hospital of the institute was merged with Kyoto University Hospital. |
| 7 | The Department of Imaging Medicine (by donations) was established (~2004.3). | |
| 1999 | 4 | The Major of Clinical Epidemiology was established in the Department of Clinical Pathologic Condition Medicine. |
| 2000 | 4 | School of Public Health (master’s program for 2 years was opened in the Graduate School of Medicine. This school consisted of four departments (Health Analysis, Health Control Sciences, Health Contributing Factor Sciences, International Health Sciences). In accordance with opening the School of Public Health, two departments of Social Medicine were closed. The Human Brain Research Center was established in the Graduate School of Medicine. |
| 2001 | 10 | The Department of Epidemiologic Data Management (by donations) was established (~2004.9). |
| 2003 | 10 | The Department of Experimental Clinical Tumor Medicine (by donations) was established (~2008.9). |
| 2004 | 4 | Kyoto University became a national university as an independent administrative entity. The Center for Genomic Medicine and Center for Medical Education were established in the Graduate School of Medicine. |
| 2005 | 4 | The Department of Immunology and Genomic Medicine (by donations) was established (~2010.3). |
| 2006 | 8 | The Department of Organ Preservation Technology (by donations) was established (~2011.7). |
| 2007 | 4 | The Department of Interdisciplinary Cancer Therapy (by donations) was established (~2012.3). The Department of Human Health Science was established in the Graduate School of Medicine. |
| 2008 | 4 | The Department of Respiratory Care and Sleep Control Medicine was established (~2013.1). |
| 4 | The School of Health Science was renamed the School of Human Health Sciences. | |
| 2009 | 4 | The Doctoral Course was established in the School of Human Health Sciences. |
| 2010 | 4 | The Term of the Department of Immunology and Genomic Medicine was extended (~2015.3). |
| 2011 | 4 | The Department of the Control for Rheumatic Diseases was established (~2014.3). |
| 7 | The Department of Target Therapy Oncology was established (~2014.6). | |
| 10 | The Department of Nephrology was established. | |
| 11 | The Bio Frontier Platform Center (Medical Support Center) was established. | |
| 2013 | 8 | The Department of Epilepsy, Movement Disorders and Physiology was established (～2018.5). |
| 2018 | 4 | Kyoto-McGill International Collaborative School in Genomic Medicine was established. |
| 12 | Professor Emeritus Tasuku Honjo was awarded the Nobel Prize in Physiology or Medicine. | |
| 2020 | 4 | Center for Cancer Immunotherapy and Immunobiology was established in the Graduate School of Medicine. |
| 2022 | 4 | Center for digital transformation of healthcare was established in the Graduate School of Medicine. |