Road infrastructure reconstruction in post-conflict South Sudan is critical to economic recovery and humanitarian access, yet its carbon footprint remains largely unquantified. This study develops and applies an integrated activity-based carbon emission estimation model for five major road reconstruction corridors totalling 510 km, encompassing the Juba–Terekeka, Malakal–Renk, Wau–Rumbek, Bor–Pibor, and Nimule–Juba routes. Emission inventories were compiled for all three GHG Protocol scopes across four major activity categories: earthworks, material production, construction equipment, and material transport. Emission factors were drawn from the IPCC 2006 and 2019 databases, PAS 2050, and EN 15804, and calibrated against local South Sudanese conditions. The aggregate construction carbon intensity was estimated at 1,369 tCO2eq per lane-kilometre, approximately 18–40% higher than comparable Sub-Saharan African road projects, attributable to long supply chains, diesel-dependent construction, and remote logistics. Monte Carlo uncertainty analysis (n = 10,000) yielded a 90% confidence interval of [556.8, 839.0] ktCO2eq for total project emissions. Sensitivity analysis identified asphalt emission factors and equipment fuel consumption as dominant drivers. Four mitigation scenarios were evaluated, with the combined strategy projected to achieve 38–52% emission reductions through low-carbon materials, equipment electrification, and optimised logistics. Policy recommendations are developed for integration into South Sudan NDC and Determined Contributions (NDCs) and the infrastructure planning framework of the Ministry of Roads and Bridges (MoRB).