Background The RTS,S/ASO1_E malaria vaccine is being piloted in three countries—Ghana, Kenya, and Malawi—as part of a coordinated evaluation led by the World Health Organization, with support from global partners. This study estimates the costs of continuing malaria vaccination upon completion of the pilot evaluation to inform decision-making and planning around potential further use of the vaccine in pilot areas. Methods We used an activity-based costing approach to estimate the incremental costs of continuing to deliver four doses of RTS,S/ASO1_E through the existing Expanded Program on Immunization platform, from each government’s perspective. The RTS,S/ASO1_E pilot introduction plans were reviewed and adapted to identify activities for costing. Key informant interviews with representatives from Ministries of Health (MOH) were conducted to inform the activities, resource requirements, and assumptions that, in turn, inform the analysis. Both financial and economic costs per dose, cost of delivery per dose, and cost per fully vaccinated child (FVC) are estimated and reported in 2017 USD units. Results At a vaccine price of $5 per dose and assuming the vaccine is donor-funded, our estimated incremental financial costs range from $1.70 (Kenya) to $2.44 (Malawi) per dose, $0.23 (Malawi) to $0.71 (Kenya) per dose delivered (excluding procurement add-on costs), and $11.50 (Ghana) to $13.69 (Malawi) per FVC. Estimates of economic costs per dose are between three and five times higher than financial costs. Variations in activities used for costing, procurement add-on costs, unit costs of per diems, and allowances contributed to differences in cost estimates across countries. Conclusion Cost estimates in this analysis are meant to inform country decision-makers as they face the question of whether to continue malaria vaccination, should the intervention receive a positive recommendation for broader use. Additionally, important cost drivers for vaccine delivery are highlighted, some of which might be influenced by global and country-specific financing and existing procurement mechanisms. This analysis also adds to the evidence available on vaccine delivery costs for products delivered outside the standard immunization schedule.