This paper scrutinizes the transformation of the higher education system in Turkey during the last decade in conjunction with the neoliberal policy agenda and protests. Neoliberalism is often understood as a reduction of the discretionary powers of the state and the government in favor of the market forces. I argue that current discussion of neoliberalization of the higher education in Turkey , in contrast, brings about centralization. Higher Education Council is at the center of the debates around this transformation. It was established in 1981 in order to place all higher education institutions under its jurisdiction as a move for centralization and the control of the higher education which was deemed necessary by the military regime at the time. From then on, university rectors are appointed by the president of Turkey based on the suggestions of the Higher Education Council which might not necessarily reflect the votes the candidates won in the university elections. The members of the Council on the other hand are mainly appointed by the President and the government (14 out of 22). A draft proposal for a transformation of the higher education system was prepared by the Higher Education Council in 2011, in reaction to which universities and some NGOs declared their opinions. This led to discussions on the policies of the JDP (Justice and Development Party) government and the role of the universities in the mass media. However, legislation discussions were not the only instances where the role of universities was put on the public agenda. It also coincided with the student protests, excessive use of violence of the police and the Prime Minister Erdogan’s responses that followed the events which focused on the legitimacy of protest as well as government interventions. Consequently this paper approaches the issue of transformation of the higher education system from three foci: state, institutional change and social movements. Framing in Student protests and different versions of Higher Education Legislation proposal drafts will be analyzed. Furthermore, content analyses of the responses from 98 universities, labor unions and NGOs like MUSIAD (Independent Industrialists' and Businessmen's Association) will be made. These analyses suggest a framework of hegemony construction and coexistence of centralization and neoliberalization.