Indonesia has introduced the National Health Insurance System or Jaminan Kesehatan Nasional (JKN) in 2014 to achieve universal health coverage by 2024. This study aimed to assess the benefit incidence of healthcare funding after the JKN implementation and its distribution by socio-economic status considering regional variation in unit costs. This analysis used Indonesia’s annual National Socio-Economic Survey and administrative data on JKN provider payments from 2015 to 2017, combined at district level for 466 districts. Findings showed that the benefit incidence of healthcare expenditure favours the wealthier groups, while substantial variation in hospital unit costs across regions was observed in Indonesia.