Background Indonesia's National Health Insurance Program, known as Jaminan Kesehatan Nasional (JKN), has a variety of membership pathways for those wishing to gain access. Claim data from JKN offers a cost-effective way of observing who is accessing healthcare services and what types of services are being used. This study is a novel attempt to measure disparities amongst JKN users in their engagement with services, providing an opportunity to reflect on patterns of use. Methods Using claims data collected from JKN users between 2015–2016, we used the Ordinary Least Square (OLS) estimation model to compare health services utilization among subsidized and non-subsidized users. We focused primarily on the individual use of the hospital for outpatient and inpatient treatment. Results Analysis reveals that subsidized users access primary healthcare services more frequently than non-subsidized users. Conversely, non-subsidized users access secondary and tertiary health care services more frequently than other users. Subsidized users who utilize secondary and tertiary health care tend to suffer more severe health illnesses than non-subsidized members. Conclusions This study concludes that income disparity affects healthcare utilization. Non-subsidized (PBPBU) members are more likely than subsidized (PBI) members to access secondary and tertiary health care services. Our study offers evidence of the potential underutilization of STHC by PBI members, which could lead to inefficiency since PBI participants seeking STHC treatment had severe health conditions, thus needing to be treated longer and requiring higher healthcare expenditures.