The seven-year system had the advantage of guaranteeing entrance to the Imperial universities at the age of Middle School.

In the later 1990s, Government and local municipalities facilitated to reform of the administrative scheme and financial management in line with economic bubble burst and financial difficulties due to Japan's progressive low birthrate and longevity.

As a result of Tokyo gubernatorial election in April 2003, Shintaro Ishihara was re-elected as Governor of Tokyo, holding up a promise "I will establish a revolutionary university", and consequently the original restructuring plan was significantly and rapidly changed, in terms of the organization of faculties, course structure, etc.

China India Indonesia Malaysia South Korea Taiwan Thailand Vietnam Turkey Australia Canada United States of America Finland Sweden Norway Ireland United Kingdom Netherlands Germany France Spain Italy Austria Poland Hungary Bulgaria Russia Lithuania Although its small size and young history in contrast to national universities and several leading private universities, the university has been one of the most reputable institutions in Japan.

The university received the highest score of 100.0 for "citations.” In 2012, Prof. Masatake Haruta was selected as a Thomson Reuters Citation Laureate as a possible winner of the Nobel Prize for his "independent foundational discoveries of catalysis by gold.