The European Union (EU) cannot make a plausible claim to sovereignty under international law. However, what the EU can do and what it also does is, is to act as if it were sovereign and claim certain rights that are considered core elements of state sovereignty. This article argues that the Court of Justice’s (ECJ) conception of the EU legal order as autonomous provides the EU with a core element of state sovereignty: jurisdictional sovereignty. Autonomy construed by the ECJ is best understood in conceptual legal and absolute terms. It is meant to shield the ECJ’s conceptual legal claims from interference. Legal autonomy as construed by the ECJ is not relative as many authors have claimed. It cannot come about in an incremental or relative manner. It cannot be based on arguments relating to the status of a self-contained regime of international law that gradually distances itself from the general rules of international law. It is a conceptual claim giving birth to the assumption of apriority that can only be made in categorical terms. In this way it is similar to sovereignty. The article first sets out how the autonomy of the EU legal order is best understood. It examines the ECJ’s case law in light of legal theoretical considerations and relates it to the separation thesis of Kelsen’s Pure Theory of Law. It then explains that autonomy is of such relevance to the EU legal order because the aprioristic character of EU law remains essentially contested. This relevance indirectly explains why the Court so cautiously protects the autonomy of the EU legal order. Finally, the article examines the Court’s reasoning in Opinion 1/17 in light of the identified absolute conception of autonomy.