Introduction Legitimacy and trust are crucial for resilient health systems in fragmented conflict zones. This study evaluates the legitimacy of public health authorities in northwest Syria under different governance models.Methods Using a deductive and inductive mixed-methods approach, the research team developed a framework with 4 indices and 18 indicators to assess the legitimacy of public health authorities that operate under different health governance models – top-down, bottom-up, and hybrid – in the context of the response to the earthquake that hit Syria in February 2023. The study includes surveys, workshops, stakeholder consultations, and an expert panel conducted in northwest Syria and online.Results The findings indicate that bottom-up health governance model is perceived as the most legitimate, followed by the mixed model, while top-down model is perceived as the least legitimate. This preference is measured across all legitimacy source indices, including legality, justification, consent and performance and across the overall Health Sector Legitimacy Index (HSLI). However, the hybrid governance approach showed limited superiority at the sub-source level regarding long-term health system response.Conclusion This study highlights the importance of considering the legitimacy of the health system in fragmented conflict zones. It helps explaining the effectiveness of the bottom-up approach and community-based governance in enhancing trust, cooperative behaviour, health interventions and achieving sustainability. Additionally, the study highlighted the role of legitimate public authorities in practising civic virtue and promoting social justice, thus contributing to peace-building efforts. These insights are crucial for policymakers and development donors to strengthen health systems in challenging contexts.