Accountability is largely referred to subjecting the decision and action of public duty bearers to some formalized/institutionalized oversight mechanisms. To guarantee that government initiatives responds to the needs of right holders in the context of governance and development. Its increased use in political and policy discourses derives from the basis that it conveys an image of transparency and trustworthiness. However, evocative powers make it also a very elusive concept because it can mean many different things to different people. The challenges facing the application of accountability in Government of South Sudan are quite significant. The presence of very weak institutions, militarized politics and patronage, ethic-based politics, a powerful executive usually associated with post-conflict states all contributes to weak accountability practices. The public bureaucracy is inefficient with inadequate much needed competencies including records keeping and reporting. In order to ensure public accountability, South Sudan must build viable, efficient, effective and professional public institution. The failure to ensure professionalism in government of South Sudan makes accountability impossible. There is too much political interference in the independence of judiciary and parliament. Members and staffs from public institutions act under duress of some sorts from the regime. This means that the oversight roles of such institutions are highly compromised. While in the old Sudan it was difficult to hold a public official whose gun was hidden under his desk to account, in South Sudan public officials and politicians veto any attempt for accountability through cleavages to ethnic/tribal power, regional, military strength to resist the power of the state. It will take a robust shift in the approach to state’s management style at all levels of government to achieve accountability in the new republic of South Sudan.