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Literature on the operation of regulatory agencies and their interactions with the executive branch of government is well established. Much less attention has been devoted to the relationship between these agencies and the courts, especially in case of judicial review of regulators’ decisions. This paper examines how judicial review of regulatory decisions produces clashes and agreements between regulatory agencies and the courts, and the influence of these relationships on regulatory governance. The research was conducted in Brazil with 21 interviews, consisting of eight officials of six federal regulatory agencies, seven attorneys from five agencies, and six federal judges. Regulatory governance, institutional theory, and regulatory overlap were the main analytical frameworks for this research. Data was subjected to content analysis. The findings showed that judicial review plays an important role in the overlapping scopes between courts and regulatory agencies. The institutional details of regulatory governance are crucial for the regulatory bodies to function. Despite the conflicts, judges seek more coordination with regulators, because of a greater awareness of the specifics of regulatory policies. Attorneys of regulatory bodies perform a key role in the dialogue between regulators and courts, especially by bridging the gap between technical and legal protocols. Regulatory litigation provides powerful economic agents with the opportunity to obtain a successful remittance of fines, thereby diluting the regulators’ ability to enforce regulation. Points for practitioners Judicial review is the only coordinating mechanism between regulatory agencies and the courts and plays a crucial role in defining regulatory policies and in controlling administrative behavior. In the process of judicial review, regulatory bodies confront the uncertainties that mark the blurred boundaries between the roles performed by state actors and authorities in dealing with regulation. By examining the Brazilian case, the research sheds light on regulatory governance and deals with the balance of power between the judiciary and formally independent regulatory bodies. The findings indicate the value of closer dialogue between regulators and courts in a context where regulatory agencies are increasingly called upon to make important technical and social choices on highly sensitive public issues.