BACKGROUND: Active and protracted conflict settings demonstrate the need to prioritise the peace through health agenda. This can be achieved by reorienting attention toward gender diverse leadership and more effective governance within health systems. This approach may enable women to have a greater voice in the decision-making of health and social interventions, thereby enabling the community led and context specific knowledge required to address the root causes of persistent inequalities and inequities in systems and societies. METHODS: We conducted a qualitative study, which included semi-structured interviews with 25 key informants, two focus group discussions and one workshop with humanitarian workers in local and international non-governmental organisations (NGOs), United Nations (UN) agencies, health practitioners, and academics, from Sub-Saharan Africa, Middle East and North Africa (MENA), and Latin America. Findings were then applied to the peacebuilding pyramid designed by John Paul Lederach which provides a practical framework for mediation and conflict resolution in several conflict-affected settings. The purpose of the framework was to propose an adapted conceptualisation of leadership to include women's leadership in the health system and be more applicable in protracted conflict settings. RESULTS: Five interrelated themes emerged. First, perceptions of terms such as gender equality, equity, mainstreaming, and leadership varied across participants and contexts. Second, armed conflict is both a barrier and an enabler for advancing women's leadership in health systems. Third, health systems themselves are critical in advancing the nexus between women's leadership, health systems and peacebuilding. Fourth, across all contexts we found strong evidence of an instrumental relationship between women's leadership in health systems in conflict-affected settings and peacebuilding. Lastly, the role of donors emerged as a critical obstacle to advance women's leadership. CONCLUSION: Continuing to empower women against social, cultural, and institutional barriers is crucial, as the emerging correlation between women's leadership, health systems, and peacebuilding is essential for long-term stability, the right to health, and health system responsiveness.