South Sudan's transition from humanitarian relief to an emerging social protection system raises a deceptively simple but politically important question: who is protected? In a country marked by conflict, displacement, climate shocks, market disruption, administrative weakness and overlapping humanitarian caseloads, the answer cannot be determined by poverty status alone. This article examines targeting, vulnerability registration and inclusion risks in South Sudan's evolving social protection architecture. It argues that the technical language of beneficiary selection hides a deeper governance dilemma: registration systems decide whose suffering becomes legible to the state and whose vulnerability remains invisible. Drawing on rights-based social protection theory, fragile-state governance literature and comparative evidence on targeting errors, the paper develops an inclusion-sensitive design model for South Sudan. The model combines categorical safeguards, community validation, mobile registration, disability and gender-sensitive outreach, grievance redress and periodic recertification. The article contributes a vulnerability-registration framework that treats databases not merely as administrative tools but as instruments of citizenship, accountability and peacebuilding. It recommends a hybrid targeting system that protects high-risk groups through presumptive eligibility while using transparent verification and appeal mechanisms to manage scarcity, reduce elite capture and build legitimacy. The paper concludes that South Sudan's social protection system will be judged not only by the transfers it delivers but by the fairness, visibility and dignity of the registration process through which vulnerable households enter the protection space.