This study focuses on institutional autonomy and the role it plays in governance and management towards enhancing the overall effectiveness of higher education systems. It addresses in particular the effect of autonomy on academic programmes, staff appointments, student admissions, administration, and financing. The study is based on case studies taken from five countries in Asia: Cambodia, China, Indonesia, Japan, and Vietnam. Each country case study investigates how national governance reforms have affected governance at the national and institutional levels. The institutions for the case studies were identified based on size, age, and implementation of reforms in the governance structure. Information from primary sources was collected through semi-structured interviews with decision-makers at national and institutional levels, based on questionnaires collected from academic and administrative staff members. The findings of the study samples indicate, among others, that increased autonomy in higher education centres around procedural matters in less developed countries, but manifests at both the substantive and procedural level in more advanced countries, such as Japan. The move towards autonomy was less successful in Indonesia, partly as a result of the perception of financial uncertainties resulting from the withdrawal of the state.