The aim of this study was to measure the costs of vector-borne disease control programs at the local level in Colombia (2016). A cost analysis was performed for this purpose from the policymaker's perspective in the municipalities (counties) of Girón and Guadalajara de Buga, specifically for the Aedes aegypti control program, the principal mosquito vector of dengue, Zika, and chikungunya. The analysis involved the quantification of all the costs required for each of the prevention and control strategies in vector-borne diseases. The costs were classified as operating and capital costs, and for purposes of comparison the costs were also calculated per case and per capita. The programs' total estimated costs were USD 146,651 in Girón and USD 97,936 in Guadalajara de Buga. Per capita cost was USD 0.88 in Girón and USD 0.99 in Guadalajara de Buga. In general, the predominant cost strategies were chemical spraying of adult mosquitos, accounting for 26% of the total costs in Girón and 47% in Guadalajara de Buga, with personnel representing 40% of the total costs for this strategy in Girón and 66% of the operating costs in Guadalajara de Buga.