Kumamoto University was established on May 31, 1949, under the National School Establishment Law that reformed the old Japanese educational system.

Since the University's inception, a number of allied schools and facilities have been incorporated and developed within its structure. These include the Center for Educational Research and School Development; the University Hospital; the Medicinal Plant Garden; the Engineering Research Equipment Center; the Center for Multimedia and Information Technologies; the Cooperative Research Center; the Institute of Resource Development and Analysis; the International Student Center; the Center for AIDS Research; the Shock Wave and Condensed Matter Research Center; the Institute of Molecular Embryology and Genetics; the Center for Lifelong Learning; the Center for Marine Environment Studies; the Research Center for Higher Education; and the Environmental Safety Center. In addition, the University operates a Kindergarten, an Elementary School, a Junior High School, and a School for Disabled Children.

Today the University has a teaching staff of about 1,000 (excluding teachers from attached schools) and a full-time student body of 8,000 undergraduates and 2,000 graduate students.