39 Squadron was founded at Hounslow Heath Aerodrome on 15 April 1916 with Royal Aircraft Factory B.E.2s and B.E.12s in an attempt to defend against German Zeppelin raids on London.

[4] Having moved to RFC Suttons Farm, 39 Squadron achieved its first success on the night of 2/3 September 1916, when Lieutenant William Leefe Robinson shot down the German Airship Schütte-Lanz SL11, being awarded the Victoria Cross for this action.

39 Squadron B.E.2 engaged Zeppelin L.33, already damaged by anti-aircraft fire, with L.33 force landing at Little Wigborough, Essex, and being destroyed by its crew.

[5] On the night of 1/2 October 1916, 2nd Lieutenant W. L. Tempest of 39 Squadron, flying a B.E.2c, spotted Zeppelin L.31 illuminated by searchlights over southwest London and shot it down with the loss of the entire airship crew.

[6][7] The squadron continued in the defence of London, supplementing its B.E.2s and B.E.12s with three Royal Aircraft Factory S.E.5s to help deal with daylight attacks by German Gotha bombers,[8] with at least one Armstrong Whitworth F.K.8 also operated by the unit.

By May that year, the squadron was fully manned and received a number of Avro 504 to train aircrew in preparation for operating more warlike aircraft.

[21] It arrived at Risalpur, North-West Frontier Province India (now part of Pakistan) at the end of January 1929, receiving its complement of twelve Westland Wapitis (which had been shipped out separately) in March that year.

[22][23] It was used for Air Policing in the North West Frontier, carrying out bombing missions against rebelling tribesmen and their villages, and support for the army.

39 Squadron was quickly committed to action against Italian East Africa, carrying out its first combat mission of the war on 12 June when a force of Blenheims attacked Dire Dawa airfield in Ethiopia, causing little damage.

[35][36] In August–September 1941, the squadron partly converted to the Bristol Beaufort torpedo bomber for anti-shipping operations, although it retained a flight of Marylands until January 1942.

[37][38] On 23 January 1942, in the first torpedo attack by the squadron, three Beauforts set out an airfield near Benghazi against an Italian convoy carrying supplies to Tripoli, Libya.

A third torpedo hit later that day by a Fairey Albacore of 826 Naval Air Squadron caused Victoria to sink.

In 1943 the unit re-equipped with Bristol Beaufighter aircraft in the ground attack role and moved back to Egypt then on to Italy.

[40] In December 1944, it re-equipped with Martin Marauders, flying medium bombing missions in support of Tito's Partisans.

As 1951 continued, tensions between the British forces in the Suez Canal Zone and the Egyptians, who wanted Britain to pull out of Egypt, and following anti-British riots in Cairo in January 1952, the squadron was put on standby to support plans for a British attack on Cairo if the situation further deteriorated, until the Egyptian army intervened and stopped the rioting, easing tensions a little.

[43] It re-equipped with Gloster Meteor NF.13 night fighters in March 1953, but following the Egyptian revolution of 1952, the situation for the British gradually became untenable, and in October 1954, the Anglo-Egyptian Agreement was signed, in which Britain agreed that its forces would leave Egypt by June 1956.

[44] The squadron moved to RAF Akrotiri on Cyprus in August 1956 as Britain and France prepared a military response to the Egyptian Nationalisation of the Suez Canal.

On 31 October, the British and French launched Operation Musketeer, a series of heavy air attacks against Egyptian targets followed by landings on 6 November.

[52] On 8 September 2003, Canberra PR.9 XH168 was written off after bursting its main landing gear tyres upon touching down at RAF Marham, with the crew suffering no injuries.

[60] The RAF crews, integrated with 42nd Attack Squadron, began training on the General Atomics MQ-9A Reaper in late 2006.

[62] On 9 April 2008, MQ-9A Reaper ZZ200 was destroyed after it made a forced landing in southern Afghanistan in order stop it from falling into insurgents hands.

Supporting intelligence specialists, Information Communications Technicians, signallers, and meteorologists bring the total number of squadron personnel to around 90.

39 Squadron was awarded the battle honour 'Afghanistan 2001–2014' (without the right to emblazon) by Her Majesty Queen Elizabeth II on 24 March 2020 due to their participation in Operation Herrick.

[70] The squadron disbanded in July 2022, with a Reaper Ground Control System returning from Creech AFB to RAF Waddington for use by No.