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Background: Effective vaccination governance in conflict-affected regions poses unique challenges. This study evaluates the governance of vaccination programs in northwest Syria, focusing on effectiveness, efficiency, inclusiveness, data availability, vision, transparency, accountability, and sustainability. Methods: Using a mixed-methods approach, and adapting Siddiqi's framework for health governance, data were collected through 14 key informant interviews (KIIs), a validating workshop, and ethnographic observations. Findings were triangulated to provide a comprehensive understanding of vaccination governance. Results: The study highlights innovative approaches used to navigate the complex health governance landscape to deliver vaccination interventions, which strengthened sub-national vaccination structures such as The Syria Immunisation Group (SIG). The analysis revealed several key themes. Effectiveness and efficiency were demonstrated through cold-chain reliability and extensive outreach activities, though formal reports lacked detailed analysis of vaccine losses and linkage between disease outbreak data and coverage statistics. Key informants and workshop participants rated the vaccination strategy positively but identified inefficiencies due to irregular funding and bureaucracy. Inclusiveness and data availability were prioritised, with outreach activities targeting vulnerable groups. However, significant gaps in demographic data and reliance on paper-based systems hindered comprehensive coverage analysis. Digitalisation efforts were noted but require further support. The SIG demonstrated a clear strategic vision supported by international organizations such as the World Health Organization, yet limited partner participation in strategic planning raised concerns about broader ownership and engagement. While the SIG was perceived as approachable, the lack of public documentation and financial disclosure limited transparency. Internal information sharing was prevalent, but public communication strategies were insufficient. Accountability and sustainability faced challenges due to a decentralized structure and reliance on diverse donors. Despite stabilizing factors such as decentralization and financial continuity, fragmented oversight and reliance on donor funding remained significant concerns. Discussion: The study highlights the complexities of vaccination governance in conflict-affected areas. Comparisons with other conflict zones underscore the importance of local organisations and international support. The SIG's role is pivotal, but its legitimacy, transparency, and inclusivity require improvement. The potential transition to early recovery in Syria poses additional challenges to SIG's sustainability and integration into national programs. Conclusion: The governance of vaccination in northwest Syria is multifaceted, involving multiple stakeholders and lacking a legitimate government. Enhancing transparency, local ownership, and participatory decision-making are crucial for improving governance. The role of international bodies is essential, emphasising the need for structured feedback mechanisms and transparent monitoring processes to ensure the program's success and sustainability. Key message: • A hybrid governance model that combines top-down and bottom-up approaches effectively improves immunisation programs in conflict settings and promotes local ownership. • In conflict settings, immunisation programmes require strong and direct intervention from the WHO with central management and coordination of the vaccine activities. • In conflict areas, when the government is a party to the conflict or has limited access to some areas, United Nations institutions must intervene to manage or support vaccine activities in partnership with local entities, regardless of notions of national sovereignty. • In Syria, the reluctance of United Nations institutions to fill the void left by the state in areas outside its control and provide vaccines led to the emergence of many diseases, including polio in 2013 and measles in 2017. [ABSTRACT FROM AUTHOR]