The article analyzes the challenges facing the security of civil aviation in the context of countering terrorism. Such challenges, which unite different sciences at the present stage, include the issue of multifaceted countering of terrorist threats. The peculiarity of such threats is that terrorism is currently an interstate phenomenon. Therefore, to protect civil aviation from terrorist threats, it is necessary to establish jurisdictional mechanisms, which have previously been used mainly under criminal law. Mechanisms of particular importance include the issue of universal jurisdiction. The universal jurisdiction, which first emerged to counter the criminal offenses of the Nazi regime, is now much more widespread. The article analyzes real cases of investigation of criminal offenses in the field of civil aviation, in situations where different countries have jurisdiction over these violations. The article concludes that in this case there can be no one universal solution to the problem and suggests real ways to solve these problems, which are applicable to different situations.