A number of national education institutions in Kumamoto Prefecture were combined to form Kumamoto University in 1949. In 2004, Kumamoto University incorporated as a national university.

The Fifth High School Founded in 1887 as the Fifth Higher Middle School. Renamed to the Fifth High School in 1894. Its main building (now the Memorial Museum of the Fifth High School), Chemical Laboratory, and main gate have been designated as important cultural properties.
Kumamoto Technical College Founded in 1897 as the Faculty of Engineering of the Fifth High School. Began operating independently as the Kumamoto Technical College in 1906. Renamed to the Kumamoto Technical College in 1944. Machinery test sites and machine tools here have been preserved from the school’s early days and are now designated as important cultural properties.
Kumamoto School of Pharmacy Founded in 1885 as the Kumamoto Pharmaceutical School . Recategorized as the Kyushu College of Pharmacy in 1910, and then as a national school in 1925. Its current configuration as a part of Kumamoto University continues to grow medicinal herbs in the Banji-en Garden that dates back to the historical Kumamoto Domain.
Kumamoto School of Medicine Founded in 1896 as a private institution to formally pass down the traditions of medical education in Kumamoto Prefecture, this school evolved into a private vocational school in 1904, then a prefectural one in 1921, before finally becoming a university in 1929.
Kumamoto Prefecture Normal School Founded in 1874 as a provisional normal school (a school for educating teachers) before being institutionalized as a prefectural school in 1878. Numerous subsequent changes in administration saw the school convert to national separate boys’ and girls’ normal schools before dividing into a youth’s normal school and the University Faculty of Education.