The principle of patient autonomy forms the foundation of medical ethics. However, its exploration within the context of national health insurance systems in developing countries remains under-researched. This study aimed to evaluate respect for patient autonomy within Indonesia's National Health Insurance (NHI/JKN) system. The study using a qualitative research interview analyzed thematically. Conducted in Depok, West Java, the study involved in-depth semi-structured interviews with 18 participants, encompassing patients from first-level health facilities (FLHF), general practitioners at FLHF, specialist doctors, and management of referral hospital (RH) officers, and staff members of the JKN. The data were transcribed and analyzed using a thematic approach. The study revealed substantial underutilization of respecting patient autonomy within medical contexts under the JKN. Five themes emerged: challenges in the referral system, knowledge and information dissemination, decision-making and autonomy, quality of healthcare services, and systemic constraints and impact. These themes highlight the lack of patient awareness, restricted medical choices, the dominant role of paternalism (a system in which the government or a person in a position of authority makes decisions for other people) in healthcare decisions, and improper informed consent process. The findings suggest that the principles of beneficence and paternalism often overshadow respect for patient autonomy in the JKN system. This raises concerns about the ethical aspect of patient treatment, particularly the need for greater focus on patient autonomy and shared decision-making to align more closely with global medical ethics practices. This study contributes to understanding autonomy in national health insurance systems in developing countries. It highlights the need for systemic reforms to enhance healthcare efficiency and effectiveness while respecting patient autonomy.