The latest version of European Union’s European Interoperability Framework (EIF 2017) introduced the concept of ‘interoperability governance’ as a key enabler of interoperability. The paper examines this concept in an information system for the judiciary. It particularly explores how the governance structure of the Integrated Administrative Court Case Management System of Greece affected the decisions regarding interoperability. We use a case study methodology to achieve this goal. Our findings are consistent, in most parts, with the conceptual model of EIF 2017. We affirm that the requirement of independence of the judiciary imposes certain limits that have to be respected in an interoperability governance structure of the courts. We emphasize on the importance of dealing with certain issues of interoperability before the introduction of an information system in the judiciary. We conclude that a ‘dynamic’ governance structure, that is a structure that changes during the life cycle of an information system, is consistent with real world challenges that arise regarding interoperability.