The increasing pace and scope of global structural change has left Japanese flagship universities at a crossroads. Reflecting upon historical trends, current policy changes and respective institutional strategies for global marketing among Japanese top research universities, the author discusses possible future directions for these institutions and how key decisions may be influenced by selected national policies. By taking a more active role in building flagship universities and making use of higher education for social and economic development, the Japanese government has already taken concrete measures to keep apace with higher education policies of neighboring Asian countries. However, in the author's view, whether or not Japan can truly develop and maintain world-class universities ultimately depends on an overall improvement in the status of East Asian higher education.