In order to strengthen their international presence, universities pursuing a world-class status are striving to increase their internationalization. Internationalization implies a transformation of university governance, especially for universities in a non-English-speaking system such as Japan's. This paper examines the challenges of internationalization for Japan's top universities as a transformation process of these universities' governance. First, the historical background of Japanese higher education as an early front-runner in Asia is discussed, along with the dynamics of national identity and global trends. Second, a series of government-funded programs for research and internationalization are examined from the viewpoint of governance reform. The construction of "world-class" universities not only implies concentrated financial investment but also a comprehensive transformation of university governance in a global context. The major challenges for top Japanese research universities in terms of maintaining and improving their international presence are also highlighted. This article suggests the importance of examining the historical and current context of university governance in East Asian higher education.