| 1884 | Kyoto Private German School was founded by the students of Dr. Rudolf Lehmann in Nakagyo-ku(then Kamigyo-ku). The Department of Pharmacy was later established as a specialized course of the school. |
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| 1892 | The Department of Pharmacy was closed and re-established as Kyoto Private Pharmaceutical School. |
| 1919 | Kyoto Private Pharmaceutical School was closed and re-established as Kyoto Pharmaceutical Professional School under the Professional School Law. |
| 1932 | The school was moved to a new campus in Misasagi, Yamashina-ku(then Higashiyama-ku). |
| 1949 | The school was reorganized as Kyoto Pharmaceutical University under the School Education Law. |
| 1965 | Master's Course in Graduate School of Pharmaceutical Studies was established. |
| 1977 | Doctoral Course in Graduate School of Pharmaceutical Studies was established. |
| 1984 | The university celebrated its centennial founding anniversary. |
| 1988 | The Institute of Molecular and Cellular Biology for Pharmaceutical Sciences (presently named as the 'S' building) was established. |
| 1999 | Master's Course in Clinical Pharmacy Studies was established. The Center for Frontier Research in Medicinal Science was established. |
| 2001 | The student hall 'Pavot' was constructed. |
| 2003 | Half of the main building 'Aigakukan' and its main lecture hall 'Aigaku Hall' on the third floor were constructed. |
| 2004 | The university celebrated its 120th founding anniversary. |
| 2005 | The remaining half of the main building 'Aigakukan' was completed. |