This comparative study addresses the critical problem of state fragility in post-independence South Sudan, arguing that persistent institutional collapse and conflict cannot be divorced from the specific governance legacies of the Sudan People’s Liberation Movement/Army (SPLM/A) insurgency. Its objective is to trace how the rebellion’s variegated administrative models, social contracts, and authority structures have shaped the fraught process of post-conflict state formation since 2011. Employing a qualitative, comparative case study design, the research utilises process-tracing and analysis of archival documents alongside fieldwork data from sub-national regions with distinct rebel governance histories. The core finding reveals a paradoxical inheritance: in areas where the SPLM/A established structured, civilian-incorporating systems, a hybrid authority foundation has provided limited local institutional resilience. Conversely, the rebellion’s wider legacy entrenched a militarised, predatory political economy that has actively undermined peacebuilding and public service delivery. The study’s central contribution is to demonstrate that the networks and institutions which secured military victory were fundamentally ill-suited for constructing an inclusive, functional state, explaining the central paradox of formal sovereignty coexisting with pervasive state collapse. These findings necessitate a recalibrated understanding of war-to-peace transitions centred on the enduring and often debilitating institutional footprints of non-state armed groups.