It was activated on 15 March 2004, after effectively redesigning its predecessor command, Allied Forces Southern Europe (AFSOUTH), originally formed in 1951.

While Admiral Robert B. Carney of the U.S. Navy was appointed as Commander-in-Chief Allied Forces Southern Europe (CinCAFSOUTH) on 19 June 1951,[5] AFMED was not activated until 1953.

The delay was due to negotiations and compromises between the Americans and the British, who wished to retain one of their commanders over Britain's traditional sea lines of communication stretching through the Mediterranean to the Suez Canal and beyond.

The initial command arrangements for AFSOUTH consisted of the classic three land, sea, and air headquarters preferred by Eisenhower.

On 14 October 1953, the Sixth Allied Tactical Air Force was also established in Izmir, commanded by Major General R.E.L.

In terms of actual forces, this meant two Greek wings, four Turkish fighter-bomber groups of F-84 aircraft, and some B-26A Mosquitoes.

The exercise included allied warships escorting three convoys of supply ships which were subjected to repeated simulated air and submarine attacks, as well as anti-submarine warfare (ASW) operations and naval gunfire shore bombardment.

[11] 1953 AFSOUTH exercises included: In 1957, Operation Deep Water simulated the defence of the Dardanelles from a Soviet attack.

Forces from Greece, Turkey and other countries in AF South Command were to participate, which is scheduled annually by CINCSOUTH.

Commander-in-Chief AFSOUTH directed the NATO peacekeeping missions in Bosnia & Hercegovina, IFOR and SFOR, from December 1995.

Beginning 10 July 1951, Headquarters Allied Land Forces Southern Europe was responsible for defending the North-Eastern Italian sector in cooperation with other NATO nations.

During the intervening 40 years, the HQ produced plans and studies to counter a potential invasion by the Soviet-led Warsaw Pact.

The reorganisation of AFSOUTH as JFC Naples in 2004 was a part of NATO’s transformation, initiated by the Prague summit of 2002, aimed at adapting the allied military structure to the operational challenges of coalition warfare, to face the emerging threats in the new millennium.

NHQ Sarajevo remains operational, as also NATO Headquarters Tirana, an outgrowth of the former Kosovo Force (KFOR) Communications Zone West, originally established in 1999.

The division HQ will be prepared to execute command and control over the NATO Force Integration Units in Romania and Bulgaria for a range of missions, which includes Article V operations based on NATO planning, when authorized by the North Atlantic Council and directed by the Supreme Allied Commander Europe.