The health system, as one of the most critical components of optimal statecraft, faces numerous challenges due to a highly centralized administrative structure. Iran’s geopolitical logic and geographical conditions necessitate consideration of a semi-centralized model as an alternative framework for governance. From the perspective of political geography, the establishment of a semi-centralized model can enhance the effectiveness of the governance system; an issue that, if not properly perceived, may generate public dissatisfaction and undermine national security. By separating stewardship from service provision functions, the semi-centralized model establishes an intelligent balance in the spatial distribution of power. Accordingly, it demonstrates notable advantages in achieving spatial justice, ensuring service quality, implementing the family physician program, and reducing per-capita health expenditures. This qualitative study aims to identify the challenges associated with implementing a semi-centralized governance model in Iran’s health system. Data were collected through semi-structured interviews with 31 experts in political geography, health governance, and public policy, and were analyzed using thematic analysis. Participants were selected through purposive sampling, and interviews continued until theoretical saturation was achieved. The findings resulted in the identification of 8 main themes, 29 sub-themes, and 177 codes, reflecting a wide range of challenges. The main themes include structural and administrative system challenges; policy-making and implementation challenges; political, security, and legal challenges; intersectoral collaboration challenges; health economics challenges; psychological and perceptual challenges; technological challenges; and cultural and social challenges. The results indicate that although the semi-centralized model has the potential to improve the effectiveness of governance in the health system, the lack of political will and insufficient coordination across different levels of governance have hindered its implementation.