Set against the backdrop of increasing economic interdependence in East Asia, the idea of “regional integration” is now being discussed as a long-term political process in the region. As in the field of the international economy, de facto integration and interdependence exist with respect to the internationalization of the higher education system in East Asia. Based on the results of a comprehensive Japan International Cooperation Agency Research Institute (JICA-RI) survey of 300 leading higher education institutions active in cross-border higher education, located in ten Association of Southeast Asian Nations (ASEAN) member Southeast Asian countries and three Northeast Asian countries (China, Japan, and Korea), this paper examines universities’ perceptions of the degree of cross-border activities, the significance of their “expected outcomes,” and their regional preferences for partners. The objective is to envision a direction for a future regional higher education framework in East Asia and to consider the policy implications of the internationalization of higher education in East Asia in the context of regionalization. The findings related to the degree of cross-border activities suggest a current perception that there is more prominent in conventional than in innovative activities, but that innovation will rise considerably in the future. With respect to the significance of “expected outcomes,” academic and political “expected outcome” are perceived to be more significant than economic “expected outcome,” which are nevertheless expected to be more significant in the future. Finally, in terms of their preferred regions of partners, universities in East Asia overall place a high priority on building partnerships within their own region. Yet, among Northeast Asian universities, North America is perceived as the most active partner.