ObjectivesThis study aimed to analyze and describe the cost of HPV vaccination program in Indonesia. MethodsThis study identified the cost-related HPV vaccination program implemented in Makassar, Manado, and Surabaya cities, Indonesia, according to the previous activities performed. Cost information was collected and analyzed in each specific activity for each cost components, using the HPV vaccination module of the World Health Organization Cervical Cancer Prevention and Control Costing tool. ResultsAccording to the Cervical Cancer Prevention and Control Costing tool, the recurrent costs, both financial and economic costs, dominated the HPV vaccination program costs in Surabaya (US dollars [USD] 264 618; USD 268 724), Makassar (USD 166 852; USD 293 300), and Manado (USD 270 815; USD 270 946), with a total cost of USD 702 285 for financial cost and USD 832 970 for economic cost. Vaccine procurement drives the recurrent cost. ConclusionsThe implementation of demonstration program in Surabaya, Makassar, and Manado cities was considerably succeed. Any prediction related to the cost of implementation of HPV vaccination in Indonesia can be calculated and used to advocate regional or national government.