Abstract: In the Area of Freedom, Security and Justice, whether the creation of the European agency tends to promote the European governance and policy delivery is a major topic with potentially far-reaching consequences for the distribution of power within the multilevel European governance. European agencies are usually expected to pool the administrative resources at European level and contribute to the institutional and policy convergence across countries. However, there is a sharp division of scholarly opinion upon this expectation between Intergovernmentalist and Neofunctionalist. To go beyond this old binary opposition, this paper takes a historical view to explore the dynamics of the interinstitutional balance involved by Frontex since 2005 and uses the Principal-Agent model to explain changes of the European border policy output. This paper concludes from the historical study that the expansion of Frontex has promoted the European policy-making and policy delivery to a more institutionalized network. Institutionalization of the border governance indicates that the Member States are not able to monopolize the rule-making and policy delivery process. More operational practice and legal changes in the Migration Crisis also confirm an indispensable functional position of Frontex in European border governance. Based on the Principal-Agent model, this paper maps the dynamics of policy output, which results from the changing interinstitutional balance driven by the increasingly powerful Frontex. This paper argues that the growing Frontex has indeed decentralized the authority of the Commission in terms of policy-making, but meanwhile, also centralized European governance upward. This paper also theoretically confirms the possibility that the relationship between intergovernmental control and supranational governance is not simply a linear trade-off. At the current stage, both supranational governance and intergovernmental control have been strengthened, at the expense of Member States’ authority.