The Taiwan Ministry of Education (MOE) put forth the aim for the top university project (ATU) in 2005 with the aim of improving the worldwide academic competitiveness and ranking performance of selected Taiwanese universities. With the conclusion of the second phase of the project at the end of 2017, this study aims to critically examine and reflect on the ministry’s fundamental assumptions regarding the idea of the world-class university (WCU) and how such an institution should be governed. To gain an in-depth and critical perspective on the policy, this study takes the form of a Foucauldian analysis. The empirical data are sourced from a range of material, including qualitative interviews, official policy documents, website resources and other relevant documents. Interview data were collected in collaboration with two MOE officials who were directly in charge of this project. This study concludes that assumptions made about the WCU by MOE officials have evolved during the last decade, indicating that the management of funding recipients is moving, in Foucauldian terminology, from top-down disciplinary power to networked governance. While higher education funding is a zero-sum game, the ATU risks creating a vicious circle in which non-ATU institutions and their students are increasingly marginalised, especially in the case of private universities. As a result, the MOE should rethink the ATU, focusing on higher education as a whole. Careful consideration of the relative advantages and disadvantages that have arisen from the launch of the ATU will help to ensure that the project is open to further improvements in the future.