Lymphatic filariasis (LF) is a vector-borne disease caused by parasitic helminths and constitutes a serious public health issue in tropical regions. According to the World Health Organization (WHO), infected cases in Southeast Asia constitute 50% of the estimated 120 million infections globally. In Indonesia, LF is caused by all filarial species, and in 2018, 236 districts from a total of 514 districts in the entire country were declared as endemic areas. The global program to eliminate filariasis has been running for the last 19 years and has been conducted as a full national initiative for the last 8 years in Indonesia. The study describes the surveillance of LF cases and prevalence in Indonesia for the past 17 years (2001-2017) – during the global and national LF elimination programs-, using national registry-based data. The data demonstrates that the national program has been largely effective in the areas it has been active the longest, while there are provinces lagging behind in the successful suppression of LF. The high geographical fragmentation of the country with the associated ecological parameters relating to LF incidence, likely play an important role in maintaining the highly varied incidence rate across Indonesia.