Meeting global and national malaria elimination targets requires identifying challenges as early as possible so that strategies can be modified to stay on track. This qualitative study of stakeholders who have a major influence on malaria programs across the Southeast Asian region, including those at a state level in India and at a national level in Cambodia, Myanmar, Thailand and Vietnam, shows that most believe Plasmodium falciparum malaria elimination targets are attainable, but are less optimistic for meeting Plasmodium vivax targets. Across these countries, stakeholders reported large variations in access to malaria diagnosis and treatment; the effectiveness of strategies for reaching migrants and hardto-serve populations; and securing sufficient numbers of skilled workers for both diagnosis and compliance with artemisinin-combination treatments and the need to optimise use of insecticides. Additionally, there was optimism about coordinated surveillance and response, but this was counterbalanced with a sense that national and regional collaboration opportunities have been missed. Climate change impacts were seen as a potential threat by all stakeholders in this study and in need of further research.