Subnational elimination aims to interrupt malaria transmission within specific geographic areas, such as administrative units. Focusing efforts on these smaller geographic regions makes achieving and sustaining zero transmission more feasible.

Subnational malaria elimination is recognised as a vital step towards achieving overall malaria elimination, as stated in the WHO Global Technical Strategy for Malaria.

Subnational malaria elimination can be an effective approach for large countries like China, India, Indonesia and countries with geographically isolated parts or islands such as the Philippines, Indonesia, and Papua New Guinea. Additionally, subnational malaria elimination is a strategy for countries near-elimination that still have areas with ongoing transmission, as is the case for Myanmar and Thailand.