This article examines the post-9/11 developments in NATO-Russia relations and Afghanistan`s role in setting the scope of their bilateral cooperation. More specifically, the article analyzes the efforts of the NATO-Russia Council (NRC), a mechanism for cooperation between NATO and Russia in fighting terrorism and insurgency in Afghanistan between 2002 and 2014. Subsequently, the paper prospectively assesses Russia’s position in relation to the post-NATO Afghanistan. NRC was established in 2002, in response to increasing concerns about terrorism after 9/11. Drawing on the positive cooperation generated by the post-9/11 fight against terrorism, NRC provided a fresh start for NATO-Russia relations, and facilitated building bridges in order to tackle new security challenges, with a special emphasis on terrorism, in the broader Euro-Atlantic region. Thus since the establishment of NRC, NATO and Russia have been cooperating more intensively. In terms of it being a safe haven for terrorists, Afghanistan immediately rose to the top of the agenda as a key issue for cooperation between NRC and Russia. Accordingly, under the NRC, NATO and Russia have actively cooperated on the stabilization of Afghanistan, and even signed transit agreements for transferring and transmitting non-military equipment through Russian territory to Afghanistan, to be used by the NATO mission (ISAF). Nonetheless, the article argues that despite the level of cooperation achieved, one can scarcely argue that this cooperation will endure. This is because, as the forthcoming NATO withdrawal shows, Russia`s post-2014 cooperation with NATO in Afghanistan will depend on the nature of the NATO mission. In this sense, Russia has expressed that for it to further cooperate with NATO in Afghanistan, NATO needs to have a valid legal basis, and UN Security Council authorization.