Since the 1990s the Thai Government has worked to reform higher education to meet a need for greater effectiveness in public universities. Long established bureaucratic systems were judged to deliver an inappropriate administrative structure, therefore, the Government formulated policies and plans to push public universities to be more autonomous. However, the shift towards greater autonomy has potential benefits and drawbacks. The primary objective of this research is to examine the impact of autonomy on the effectiveness of Thai universities using an institutional theory perspective. The study adopts a qualitative, interpretivist methodology using a case study approach. Three Thai universities with distinctive backgrounds and at different stages of adopting an autonomous form were identified and chosen. The data was collected through a series of extensive, face-to-face semi-structured interviews with key senior members of each of the three case universities. Information was also collected from the Government sources, public information and from internal organisational records. The research findings indicated that the influences of institutional pressures play a significant role in how each university adopts an autonomous model. While autonomy has brought benefits to the universities in terms of flexibility, it also has brought some challenges. The autonomous model has increased the level of complexity within the universities in terms of structure and administrative process. The level to which the university achieves the Government missions varies depending on how well it can adapt to the autonomous model. Two out of three case studies, are able to effectively adapt to the autonomous model, achieve the Government missions at higher level, while the other that is struggling to adapt, achieves at lower level. Historical root, identity and leadership are important variables in determining such different outcomes in the case studies. The analysis of the case studies suggests that the meaning of effectiveness is shaped by institutional factors and that universal forms of structure and governance in every university may not be appropriate. This research concludes that rather than a focus on developing a standard autonomous form, the emphasis should be on standardisation of outcomes while allowing some measure of flexibility in how autonomy is interpreted in the structure and processes of each university.