The North Atlantic Alliance has been present in North Macedonia since 1999 as a result of the Kosovo crisis. In 2002, NATO Headquarters in Skopje (NATO HQSk) was formed, which has so far had a maximum of 300 people employed. Owing to the progress made with regard to defence reforms in North Macedonia (at the Summit in Bucharest in 2008 it was decided that Macedonia would be invited into NATO as soon as it resolved its dispute over the name of the country with Greece) and reduction of needs for rear support in Kosovo, NATO presence is being reduced in North Macedonia as well.

The most important NATO HQSk tasks are to support North Macedonia in the process of transforming defence and security sector and to assist the country on its way to becoming a NATO member. In this respect, NATO HQSk developed an intensive cooperation with the North Macedonian Ministry of Defence, the Ministry of the Interior and the Ministry of Foreign Affairs. Together with the North Macedonian Ministry of Transport and Communication it coordinates NATO's implementation of the programme for the reconstruction of road infrastructure in Macedonia (co-financing the construction of roads and bridges). NATO HQSk is also tasked with supporting NATO operations and missions in the Western Balkans (especially KFOR) and the monitoring of the implementation of the Ohrid Framework Agreement which was signed following the 2001 inter-ethnic conflict among the representatives of the Albanian community and Macedonia.

Slovenia has participated in NATO HQSk since November 2009, when one servicemember was deployed to NATO's Advisory Team (logistics).