Since 2004, all national universities in Japan have been transformed into “national university corporations”. Due to its long history, large scale and international competitiveness, the University of Tokyo has been regarded as a representative university before and after this important reform. Through document analysis, this paper discussed its internal and external situation of national university incorporation, and examined its effects during the first cycle of national university corporation evaluation (2004~2009). Four conclusions could be drawn from the study. 1. Since WWII, the Japanese government has been trying to conduct national university incorporation. Due to the policy of reducing the number of civil servants, the education authority and representative universities, such as the University of Tokyo, shifted their positions and led all the national universities to get incorporated in 2004. 2. Some external reasons, such as “Toyama Project” and “Five-University Alliance in Tokyo”, forced the University of Tokyo to face the reality and launch “UT21 Conference” and “The Charter of Todai” in order to prepare itself for university incorporation. 3. In the first cycle of university corporation evaluation, the University of Tokyo had only two items assessed as “excellent”; however, its dependence on government subsidy and its personnel fee were reduced more than the other universities’, indicating the increased effectiveness of its management. 4. Although the University of Tokyo has made a good progress in research and teaching since national university incorporation, it regressed in “Times Higher Education Supplement Ranking” in 2009 and 2010. This study concluded that it is not easy for a university to maintain a high position in world-wide university rankings after university incorporation.