The health supply chain, as the backbone of access to medicines, vaccines, and medical equipment, faces pressures in Iran such as intermittent shortages, institutional fragmentation, and environmental constraints. However, many of these problems are not merely technical or operational; they are rooted in the way governance is structured, how authority is distributed, and the rules that shape decision-making. This study aims to analyze the governance of Iran’s health supply chain with a focus on roles, authorities, and decision-making mechanisms. A mixed-methods design was employed. In the qualitative phase, the Critical Systems Heuristics framework and its twelve boundary questions were used; data were collected through semi-structured interviews with 18 experts and key stakeholders in the health supply chain and analyzed by comparing the “current state” with the “desired state.” Subsequently, the Best–Worst Method was applied to prioritize the extracted components. The findings indicate that governance challenges are primarily related to four dimensions: the dominance of a logistics-oriented and short-term perspective, unclear roles and overlapping authorities, weak accountability and limited representation of affected stakeholders, and a prevailing reliance on administrative data and procedures over field experience. The weighting results further suggest that improving health supply chain governance requires re-framing the problem and redefining the supply chain’s position within health governance, clarifying roles and authorities, strengthening participation and accountability mechanisms, and institutionalizing evidence-informed learning based on implementation feedback.