Background: The challenges of universal health coverage (UHC) in developing countries with a significant proportion of the labor force that works in the informal sector include administrative difficulties in recruiting, registering and collecting regular contributions in a cost-effective way. As most developing countries have a limited fiscal space to support the program in the long run, the fiscal sustainability of UHC, such as that in Indonesia, relies heavily on the contributions of its members. The failure of a large proportion of voluntary enrollees/self-enrolled members/informal sector workers (Peserta Mandiri/Pekerja Bukan Penerima Upah [PBPU] members) to pay their premiums may lead to the National Health Insurance System (NHIS) in Indonesia being unable to effectively deliver its services. Objective: This study aims at exploring the important factors that affect the compliance behavior of informal sector workers (PBPU members) in regularly paying their insurance premium. This analysis may be a basis for designing effective measures to encourage payment sustainability in informal sector workers in the NHIS. Method: This study utilizes the survey data collected from three regional offices of the Indonesian Social Security Agency for Health (SSAH), which cover approximately 1210 PBPU members, to understand the relationship between members’ characteristics and their compliance behavior regarding the premium payment. We applied an econometric analysis of a logit regression to statistically estimate which factors most affect their compliance behavior in paying the insurance premium. Results: This study reveals that almost 28% of PBPU members do not pay their insurance premiums in a sustainable way. Our logistic regression statistically confirms that the number of household members, financial hardship, membership in other social protection arrangements, and the utilization of health services are negatively correlated with the compliance rate of informal sector workers in paying their insurance premium. For instance, people who experience financial hardship tend to have a 7.7 percentage point lower probability of routinely paying the premium. In contrast, households that work in agricultural sectors and have income stability, the cost of inpatient care incurred before joining the NHIS, a comprehensive knowledge of the SSAH’s services, and the availability of health professionals are all positively correlated with regular premium payment. Conclusion: Although there is no single policy that can ensure that informal sector workers (PBPU members) regularly pay their premiums, this study recommends some policy interventions, including (1) flexibility in applying for a government subsidy for premiums (Penerima Bantuan Iuran [PBI]), especially for people who have financial hardship; (2) an intensive promotion of insurance literacy; (3) expanding the quantity and quality of healthcare services; and (4) tailor-made policies for ensuring the sustainability of premium payments for each regional division.