The North Atlantic Treaty Organization (NATO) and the Shanghai Cooperation Organization (SCO) are two important regional security organizations covering interrelated areas, yet they do not cooperate in the area of counter-terrorism. The comparative analysis of their counter-terrorism efforts can bring a fresh perspective beyond that of inter-block rivalry by adding a layer of complexity while evaluating the advantages of cooperation. In this article, the counter-terrorism efforts of NATO and the SCO are compared with regard to their founding principles, legal doctrines, organizational structures and military operations. It provides analysis of how these organizations created their legal doctrines, established their organizational structures and implemented practices in combating terrorism. Based on this comparison, it was discovered that both organizations transformed and adapted to better fight terrorism following the 9/11 terrorist attacks; however, due to the differences in their founding principles, NATO and the SCO tackled terrorism via different paths. Since terrorism is their common enemy, it can be asserted that collaboration between NATO and the SCO would benefit the counter-terrorism efforts of both organizations, as well as global efforts.