In this paper, I argue that there is clear evidence of neglect of higher education in post-independent South Sudan. The study, therefore, interrogates the scope of the higher education crisis in the country and assesses prospects for change from the standpoint of equity and quality using institutionalism as a theoretical framework. The study points out that the crisis of the system runs through the tapestry of South Sudan’s history of state formation against which the variable of nation-building at the dawn of Independence in 2011 has failed to assign adequate value for higher education in the pursuit of the objectives of national transformation in particular, and modernisation in general. It remains to be seen if the political leadership and the academic community could define the payload of South Sudan’s higher education system as the country transitions into a constitutional democracy capable of according greater autonomy and initiative to its universities; and revisiting the whole gamut of post-secondary education in order to render it more responsive to addressing the needs of society, particularly in non-academic streams of learning. Besides the historical and institutional challenges, the higher education system of South Sudan must expedite its internationalisation as its formative years wane out. The fundamental requirement is for its competent and dynamic scholars to lead a spirited dialogue and concerted action that should not be broken off by recurrent political violence. This is a must if South Sudan is to stand on the cusp of real transformation in its higher education landscape.