Decades of civil conflict have left South Sudan with one of the most severely degraded road networks in sub-Saharan Africa, with fewer than 250 km of paved roads across a country of approximately 644,329 km². The post-conflict reconstruction challenge is compounded by severely constrained public financial resources, complex political geography, and extreme seasonal flooding that renders up to 40% of the road network inaccessible for extended periods. Effective prioritisation of limited rehabilitation budgets across competing road segments demands a rigorous, transparent, and defensible decision framework. This study develops and applies a Multi-Criteria Decision Analysis (MCDA) framework integrating the Analytic Hierarchy Process (AHP) with a Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) to prioritise road rehabilitation investments across 32 candidate road segments in South Sudan’s Central Equatoria, Jonglei, and Upper Nile states. Six evaluation criteria are considered: road condition index (RCI), traffic volume (AADT), socio-economic connectivity, flood vulnerability, cost-benefit ratio, and post-conflict accessibility urgency. AHP-derived weights are validated through sensitivity analysis and expert panel consultation (n = 7 engineers). The MCDA framework identifies 8 high-priority segments totalling 412 km and estimates optimal allocation of a hypothetical USD 180 million rehabilitation budget. Results are validated against Independent Roads Needs Assessment (IRNA) survey data, achieving 81.3% ranking concordance. The framework provides a replicable, evidence-based decision support tool for the Ministry of Roads and Bridges (SSNRA) and international development partners.