: Petroleum pipeline crossings over road corridors represent structurally critical and economically vital infrastructure intersections in South Sudan, a nation where oil revenues constitute more than 90% of government income and where national road networks are subjected to severe seasonal flooding driven by the Sudd wetland hydrological system and intensifying climate variability. This study presents a comprehensive structural assessment framework for both aerial and buried petroleum pipeline crossings over flood-prone road corridors in South Sudan's three principal oil-producing states: Jonglei, Upper Nile, and Unity. Using three-dimensional finite element modelling (FEM) in ABAQUS/Standard, limit state design analysis, scour depth estimation, and field-calibrated hydraulic loading, eight representative crossing sites were evaluated under governing combined load combinations incorporating dead loads, traffic loads, hydrodynamic flood forces, internal operating pressure, and cyclic Vertisol shrink-swell soil loads. Results indicate that unanchored aerial crossings at Jonglei sites experience maximum Von Mises stresses of up to 312 MPa — reaching 87% of the API 5L Grade X52 yield strength — under peak flood and wind loading. Buried crossings are subjected to scour depths of 1.9–2.8 m that exceed minimum burial requirements and generate net uplift forces of up to 4.4 kN/m. A novel composite Pipeline-Road Crossing Vulnerability Index (PRCVI) is proposed, integrating structural, hydraulic, and geotechnical parameters through an Analytical Hierarchy Process (AHP)-weighted formulation. The PRCVI classifies two sites as High Risk and two as Moderate Risk, providing a scalable prioritisation tool for the SSNRA and pipeline operators. Targeted rehabilitation recommendations are