Purpose The purpose of this paper is to examine the role of Association of Southeast Asian Nations’ (ASEAN) flagship universities in moving the agenda of regional integration forward through academic/research collaboration and cooperation. Design/methodology/approach Flagship universities are leading universities in the national higher education systems of countries that make up the ASEAN. This study on the ASEAN’s flagship universities is based on a three-pronged strategy, namely, a literature review, analysis of websites contents, and citation of supporting pieces of evidence from other relevant studies to support arguments. Using the QS top universities in Asia 2016 listing, top 70 public universities in ASEAN were selected for investigation. In instances where public universities in a particular ASEAN country were not listed in the QS listing, a premier public university of that country was then selected for investigation. Findings There is a tendency for ASEAN’s flagship universities to look beyond ASEAN, primarily to establish vertical collaboration, which is important to their efforts in creating their image and enhancing their reputation. As a result, academic/research collaboration among flagship universities and collaboration between these universities and other universities in ASEAN is glaringly on the low side. Interestingly, to move the regional integration agenda in ASEAN, other intermediary agencies outside of ASEAN, such as in the European Union, are very active in providing a platform for both flagship and non-flagship universities to collaborate. Originality/value While regional collaboration and cooperation within ASEAN and East Asia have been discussed elsewhere, this paper has utilised and expanded Douglass’ (2016) idea of flagship universities to include regional relevance for the purpose of regional integration of ASEAN.