Background: The governance of childhood vaccination in crisis-affected populations presents distinctive and intricate challenges and has been criticized for being inadequate. In this study, our aim was to investigate the existing practices related to decision-making on vaccination in crisis-affected settings and develop practical suggestions for enhancing these. Methods: We followed a qualitative research approach, conducting 31 remote semi-structured interviews with individuals involved in humanitarian vaccination efforts and stakeholders operating at global, regional, and national levels. We used a thematic approach using a mix of inductive and deductive coding to analyse the data while applying the Governance Analytical Framework (GAF). Results: Our research indicates that decision-making in crisis-affected settings suffers from a lack of structure, documentation, and transparency. Participants highlighted the presence of diverse and conflicting agendas among different stakeholders and the insufficiency of timely, reliable data crucial for effective decision-making. As solutions, participants recommended improved coordination among stakeholders and emphasized the need for meaningful engagement of local actors. Conclusion: The study uncovered a fragmented, disorganised and complex governance landscape of vaccination services in crisis-affected settings spanning multiple levels and involving various actors. To improve this landscape, it is crucial to intensify efforts to ensure fairness, accountability and effectiveness.