Rectors of Kazakhstani universities are being asked to move towards a system of greater institutional autonomy through the development of new governance structures, such as the creation of boards of trustees and to pursue greater quality through international partnerships and international accreditation. However, this push for change is occurring within a system that continues to embrace the value of hierarchy and regulation. Even Nazarbayev University, which is exempt by law from Ministerial oversight and which is supported by sustained partnerships with elite universities from other nations finds itself facing significant challenges. The purpose of this paper is to describe the process of learning autonomy within a system that continues to be shaped by the regulatory and cultural forces of a centralized system. The paper is based on a qualitative study undertaken by researchers at the University of Pennsylvania and Nazarbayev University and involved conducting interviews with senior administrators, faculty members and students at nineteen post-secondary institutions in five cities in Kazakhstan.