Established in 2001, the Judiciary Counterintelligence Center is responsible for protecting judicial independence and maintaining security in the Judiciary. Its establishment is based on the constitutional powers of the Head of the Judiciary rather than on a law passed by Parliament. Because of this, the Center faces important legal challenges. In this context, two fundamental challenges can be mentioned. Firstly, the Center’s charter is not publicly available. Secondly, although the Center was established to protect judicial independence, it focuses on the institutional independence of the Judiciary and does not pay enough attention to the personal independence of judges. The Center also faces structural challenges because its personnel at every organizational level are appointed by senior Judiciary officials who are outside the Center. This may affect the Center’s independence. In addition, prosecutors and counterintelligence officers oversee each other’s work, which can create potential problems. There are, too, concerns about the legality of the Center’s powers. For example, the Head of the Center is a member of the Intelligence Coordination Council despite the fact that the Law on the Establishment of the Ministry of Intelligence does not allow this. The Center also acts as judicial police without any legislative authorization. Finally, there are two functional challenges. First, the Center’s responsibilities are not clearly defined. Secondly, it sometimes comes into conflict with other intelligence agencies. This article argues that these challenges may affect the Center’s legitimacy and effectiveness. Accordingly, it suggests that Parliament pass a comprehensive law to resolve these challenges.