It was founded in November 1857 as Medical Training Institute (医学伝習所, Igaku denshūsho) by the branch office of Tokugawa Shogunate.

The first professor was J. L. C. Pompe van Meerdervoort, and the institute was one of the first[3] western-style (not Kampō) medical schools in Japan.

The Institute of Tropical Medicine (長崎大学熱帯医学研究所], NEKKEN or NUITM) was originally founded under Nagasaki Medical College to perform basic and applied studies on endemic diseases in East Asia.

In 1949, the institute merged with other facilities to form Nagasaki University under the new ruling of the National School Establishment Law.

[17] With over one hundred graduate students enrolled, NUITM carries out an extensive capacity strengthening program in counterpart countries, and collaborates with a large network of institutions in Africa,[18][19] South America, and Asia through MEXT, Japan International Cooperation Agency (JICA),[20] Official Development Assistance (Japan) (ODA), Japan Agency for Medical Research and Development (AMED) and the WHO.

[22] The institute also offers a Joint PhD Programme for Global Health as part of an academic partnership with the London School of Hygiene and Tropical Medicine.

[26] Researchers at NUITM, in collaboration with local public health institutes, initiated efforts in diagnosing SARS-CoV-2,[27] including developing new diagnostic tools.

It was the fourth national commercial college in Japan, after Tokyo (1887), Kobe (1902) and Yamaguchi (February 1905), and aimed at educating students so that they could engage in business with China, Korea and Southeast Asia.