Background: Adopting Universal Health Coverage for implementation of a national health insurance system [Jaminan Kesehatan Nasional (JKN)/Badan Penyelenggara Jaminan Sosial or the Indonesian National Social Health Insurance Scheme (BPJS)] targets the 255 million population of Indonesia. The availability, accessibility, and acceptance of healthcare services are the most important challenges during implementation. Referral behavior and the utilization of primary care structures for underserved (rural/remote regions) populations are key guiding elements. In this study, we provided the first assessment of BPJS implementation and its resulting implications for healthcare delivery based on the entire insurance dataset for the initial period of implementation, specifically focusing on poor and remote populations. Methods: Demographic, economic, and healthcare infrastructure information was obtained from public resources. Data about the JKN membership structure, performance information, and reimbursement were provided by the BPJS national head office. For analysis, an ANOVA was used to compare reimbursement indexes for primary healthcare (PHC) and advanced healthcare (AHC). The usage of primary care resources was analyzed by comparing clustered provinces and utilization indices differentiating poor [Penerima Bantuan Iur (PBI) membership] and non-poor populations (non-PBI). Factorial and canonical discrimination analyses were applied to identify the determinants of PHC structures. Results: Remote regions cover 27.8% of districts/municipalities. The distribution of the poor population and PBI members were highly correlated (r2 > 0.8; p < 0.001). Three clusters of provinces [remote high-poor (N = 13), remote low-poor (N = 15), non-remote (N = 5)] were identified. A discrimination analysis enabled the >82% correct cluster classification of infrastructure and human resources of health (HRH)-related factors. Standardized HRH (nurses and general practitioners [GP]) availability showed significant differences between clusters (p < 0.01), whereas the availability of hospital beds was weakly correlated. The usage of PHC was ~2-fold of AHC, while non-PBI members utilized AHC 4- to 5-fold more frequently than PBI members. Referral indices (r2 = 0.94; p < 0.001) for PBI, non-PBI, and AHC utilization rates (r2 = 0.53; p < 0.001) were highly correlated. Conclusion: Human resources of health availability were intensively related to the extent of the remote population but not the numbers of the poor population. The access points of PHC were mainly used by the poor population and in remote regions, whereas other population groups (non-PBI and non-Remote) preferred direct access to AHC. Guiding referral and the utilization of primary care will be key success factors for the effective and efficient usage of available healthcare infrastructures and the achievement of universal health coverage in Indonesia. The short-term development of JKN was recommended, with a focus on guiding referral behavior, especially in remote regions and for non-PBI members.