BackgroundThe role played by regional organisations in climate change adaptation and health is growing in Southeast Asia, with the Asian Development Bank and the Asia-Pacific Regional Forum on Health and Environment both supporting health and adaptation initiatives. There is, however, a lack of empirical research on the value that regional organisations add to national health-related adaptation. This qualitative research compares regional project and governance-based models of adaptation and health support in Southeast Asia, providing an analysis of strengths and weaknesses of each, as well as possibilities for improvement. MethodsAn existing adaptation assessment framework was modified for this research, and used as a guide to gather and analyse data from academic and grey literature, policy documents and interviews in order to qualitatively assess two organisations and their different models of adaptation and health support.ResultsThis research found differing strengths in the approaches to climate change and health used by the Asian Development Bank and by the Asia-Pacific Regional Forum on Health and Environment. The regional forum has vision, high levels of perceived legitimacy, and access to ‘in-house’ expertise in public health and climate change. Conversely, the Asian Development Bank has strengths in project management and access to significant financial resources to support work in climate change and health.ConclusionWhen regional organisations, such as the Asian Development Bank and the Asia-Pacific Regional Forum on Health and Environment, have membership and mandate overlaps, their work will likely benefit from well designed, institutionalised and incentivised coordination mechanisms. Coordination can reduce redundancies as well as the administrative workload on partner government agencies. In the case-study examined, the Asian Development Bank’s project management expertise complements the vision and high levels of perceived legitimacy of the Asia-Pacific Regional Forum on Health and Environment, thus a coordinated approach could deliver improved adaptation and health outcomes.Electronic supplementary materialThe online version of this article (10.1186/s12992-018-0388-z) contains supplementary material, which is available to authorized users.