This study investigates the administrative barriers hindering equitable educational access for marginalized communities in South Sudan, focusing on rural populations, internally displaced persons (IDPs), and girls. Despite constitutional guarantees to education, systemic inefficiencies, corruption, and inadequate policy implementation perpetuate exclusion, particularly in conflict-affected regions. Employing a mixed-methods approach, the research combines surveys with 450 households across three rural counties, in-depth interviews with 30 IDP families, and focus group discussions with 60 school-aged girls and education stakeholders. Findings reveal that bureaucratic delays in school registration, inequitable resource allocation, and gender-biased administrative practices disproportionately disadvantage rural communities, IDPs, and girls. For instance, 68% of rural schools lack government-recognized teachers, while 72% of IDP children face documentation barriers to enrollment. Girls encounter additional hurdles, including discriminatory fee structures and inadequate sanitation facilities, contributing to a 40% dropout rate. The study highlights how administrative failures intersect with socio-cultural norms to deepen educational inequities. These insights underscore the urgent need for decentralized governance, anti-corruption measures, and gender-responsive policies to align administrative practices with South Sudan’s equity goals. By centering African voices and contextual realities, this research contributes to broader debates on education governance in post-conflict settings, offering actionable recommendations for policymakers and NGOs working to dismantle structural barriers to inclusive education.