This mixed-methods study investigates the nexus between protracted armed conflict and the health system in South Sudan, analysing patterns of destruction, the political economy of reconstruction, and the governance challenges that perpetuate fragility. Quantitative analysis of conflict event and health facility data from 2013–2023 reveals a significant, non-random correlation between conflict intensity and the degradation of primary healthcare infrastructure. Qualitative findings, drawn from elite interviews and policy document analysis, demonstrate how reconstruction efforts are co-opted by patronage networks, undermining equitable service delivery and institutional legitimacy. The integrated discussion argues that the health system functions as both a casualty and a conduit of political contestation, where governance failures are not merely a consequence but a core mechanism of the conflict itself. The conclusion offers policy-relevant insights for moving beyond technical fixes towards politically informed health system governance in conflict-affected states.