Introduction <p>Hospital governance is crucial for ensuring the quality of care and patient safety. Despite numerous reforms in hospital governance accountability structures in Iran, some challenges persist. This study identifies the challenges of governance accountability structures in Iranian hospitals from the perspectives of administrators and policymakers.</p> Methods <p>This qualitative study used semi-structured interviews with 23 hospital administrators and governance experts in Iran. Participants were selected through purposive sampling. Interviews were conducted face-to-face, online, or by phone, and data were analyzed using thematic analysis based on Braun and Clarke’s framework.</p> Results <p>The study identified two main themes: governance structure challenges and accountability structure challenges. Governance structure challenges included internal issues such as the lack of a medical staff council, presidential governance, and the dominance of physicians, as well as external matters like centralization and rigid regulations. Accountability challenges encompassed administrative, financial, and socio-political dimensions, with issues such as the preference for personal relationships over accountability, centralized planning, and political pressures affecting hospital operations.</p> Conclusion <p>The study highlights the need for reforms in Iranian hospital governance and accountability structures. Recommendations include forming boards of trustees and medical staff, decentralizing decision-making, and revising regulations to improve clinical, financial, and socio-political accountability. These changes could enhance the overall governance and accountability of Iranian hospitals.</p>