In Brazil, the right to health claimed by indigenous peoples interacts with various regulatory milestones, including the Alma-Ata Declaration, which proposes and highlights primary health care (PHC) as a means to increase access and minimize health inequalities. As part of the Brazilian Unified Health System (SUS), an indigenous health subsystem (SASI) was established, along with a National Policy for the Care of Indigenous Peoples (PNASPI), as a strategy to ensure health care access for these populations. PNASPI aims to provide differentiated health care to indigenous populations, considering the sociocultural diversity and the epidemiological and logistic peculiarities associated with the care of these peoples and focusing on the provision of comprehensive care. The present article discusses the implementation of PNASPI, highlighting achievements and challenges faced during this process. Despite the growing financial resources made available for the implementation of the indigenous health subsystem, the initiatives developed thus far have had little impact on health indicators, which reflect historical inequalities in relation to other population segments. Indigenous social control is still fragile, and the discussions in this arena show the dissatisfaction of users toward the system. The discontinuity of care, added to the shortage of and high turnover of health care workers and the need to establish intercultural dialogues that promote articulation with traditional knowledges, challenge the effectiveness of PNASPI. Care is still centered on palliative and emergency measures, usually based on relocation of patients for treatment, which is associated with high cost. To overcome these challenges, PHC must be strengthened and recognized as a regulatory milestone by the PNASPI organizational model.