Kitasato University School of Medicine (KUSM) was founded in 1970 as the first Japanese medical school built after World War II. Established in the wake of the student uprising that took place in Japanese universities at the end of the 1960s, KUSM introduced an innovative educational system that was a radical restructuring of the traditional medical school curriculum. This novel method combining general medical education, collaborative research, and patient care came to be known as the Kitasato System, and it had a strong influence on other academic institutions in Japan during the 1970s.
KUSM has 13 academic units in Basic Medical Sciences and 28 in Clinical Medical Sciences:

Kitasato University was founded in 1962 to commemorate the 50th anniversary of The Kitasato Institute. The University initially consisted of one school and two departments, but now it comprises seven graduate schools, seven undergraduate schools, one college, three affiliated research institutes, and three hospitals.

Kitasato University has six campuses spread throughout Japan:
- Shirokane Campus in Tokyo
- Sagamihara Campus in Kanagawa
- Kitamoto Campus in Saitama
- Towada Campus in Aomori
- Sanriku Campus in Iwate
- Niigata Campus in Niigata
The University has its headquarters in Shirokane where the School of Pharmaceutical Sciences is based, but the major educational facility is located in Sagamihara. The Sagamihara Campus is home to the School of Medicine, the School of Nursing, the School of Science, the School of Allied Health Sciences, the Center of Liberal Arts and Sciences, and Kitasato University Hospital.

The present Kitasato Institute was established in 2008 through the integration of the former Kitasato Institute and Kitasato University. It was originally founded in 1914 by Dr Shibasaburo Kitasato as Japan's first private medical research facility. Together with Germany's Robert Koch Institute and France's Pasteur Institute, The Kitasato Institute has become one of the world's top microbiology institutes. Headquartered in Shirokane, Tokyo where it was founded, the Institute administers Kitasato University as well as two vocational schools and two affiliated institutions. As Japan's only academic organisation to possess facilities for vaccine production, the Institute contributes to the eradication of infectious diseases and the improvement of public health.