Abstract This paper maps emerging trends and South‐South cooperation in regional knowledge networks through a bibliometric analysis of avian influenza research in Southeast Asia, between 2004 and 2019. The findings indicate that a substantial research output involving researchers and organisations in the region was generated. However, wide disparities between countries existed, both in terms of output and participation in the regional network, which was largely driven by non‐regional actors. A more proactive involvement of institutions for regional cooperation such as the Association of Southeast Asian Nations (ASEAN) would increase local ownership, sustainability and redress imbalances in the regional research system.