Background : Over the past few years, the capacity of the government of Mozambique to sustain the operational cost of Indoor Residual Spraying (IRS) is facing numerous challenges due to restrictions of the Official Development Assistance (ODA), an external aid scheme of financing from the Mozambican government budget. Objectives: The objective of the study was to estimate the cost of IRS operationalization in two districts of Maputo Province (Matutuíne and Namaacha) in Mozambique, in 2014. Methods: The cost analysis followed an “ingredients based” approach from the provider perspective. The cost information was collected retrospectively, and both economic and financial costs were calculated. Results were tested using a “one-way” deterministic sensitivity analysis. Results : From the economic analysis, Matutuíne and Namaacha on average totaled an annual economic cost of US$117,351.34, with an average economic cost per household sprayed of US$16.35, and an average economic cost per person protected of US$4.09. In the financial analysis, both districts faced an average total annual financial cost of US$69,174.83, an average financial cost per household sprayed and per person protected of US$9.84 and US$2.46, respectively. Our findings indicate that vehicles, personnel salaries, and IRS consumables were components with a substantial cost for IRS operationalization. Conclusions : For our results, with resource constraints, it is important to focus on operationalizing IRS within the available budget by respecting the right timing for scheduled IRS spraying rounds and by paying attention to cost drivers in order to reduce the costs.