Background: Dengue is associated with significant economic expenditure and it is estimated that the Asia Pacific region accounts for >50% of the global cost. Indonesia has one of the world's highest dengue burdens; Aedes aegypti and Aedes albopictus are the primary and secondary vectors. In the absence of local data on disease cost, this study estimated the annual economic burden during 2015 of both hospitalized and ambulatory dengue cases in Indonesia. Methods: Total 2015 dengue costs were calculated using both prospective and retrospective methods using data from public and private hospitals and health centres in three provinces: Yogyakarta, Bali and Jakarta. Direct costs were extracted from billing systems and claims; a patient survey captured indirect and out-of-pocket costs at discharge and 2 weeks later. Adjustments across sites based on similar clinical practices and healthcare landscapes were performed to fill gaps in cost estimates. The national burden of dengue was extrapolated from provincial data using data from the three sites and applying an empirically-derived epidemiological expansion factor. Results: Total direct and indirect costs per dengue case assessed at Yogyakarta, Bali and Jakarta were US$791, US$1,241 and US$1,250, respectively. Total 2015 economic burden of dengue in Indonesia was estimated at US$381.15 million which comprised US$355.2 million for hospitalized and US$26.2 million for ambulatory care cases. Conclusion: Dengue imposes a substantial economic burden for Indonesian public payers and society. Complemented with an appropriate weighting method and by accounting for local specificities and practices, these data may support national level public health decision making for prevention/control of dengue in public health priority lists.