Background Mass drug administration (MDA) has received growing interest to accelerate the elimination of multi-drug resistant malaria in the Greater Mekong Subregion. The potential effectiveness of delivering targeted MDA was demonstrated in a recent intervention in Kayin State, Myanmar. Policymakers and funders need to know what resources are required if MDA is to be included in elimination packages beyond existing malaria interventions. Methods We used financial data from a malaria elimination initiative, conducted in Kayin State, to estimate the programmatic costs of the MDA component using a micro-costing approach. Three activities (community engagement, identification of villages for MDA, and conducting mass treatment in target villages) were evaluated. We then estimate the programmatic costs of implementing targeted MDA to support P. falciparum malaria elimination in Kayin State. A costing tool was developed to aid future analyses.Results The cost of delivering MDA within an integrated malaria elimination initiative in Eastern Kayin State was approximately US$ 910 000. The cost per person reached for MDA was US$ 2·5. Conclusion This cost analysis can assist policy makers in determining the resources required to clear malaria parasite reservoirs. The analysis demonstrated the value of using financial data from research activities to predict programmatic implementation costs of MDA in different numbers of target villages.