Formed during World War I at Fort Grange, Gosport on 1 March 1916 as Number 45 Squadron, the unit was first equipped with Sopwith 1½ Strutters which it was to fly in the Scout role.

Deployed to France in October of that year, the Squadron found itself suffering heavy losses due to the quality of its aircraft.

Transferred to the Austro-Italian front at the end of 1917, 45 Squadron there engaged in ground attack and offensive patrols until September 1918 when it returned to France and joined the Independent Force.

They included future Air Vice-Marshal Matthew Frew, Cedric Howell, Geoffrey Hornblower Cock, future Air Commodore Raymond Brownell, John C. B. Firth, Kenneth Barbour Montgomery, Mansell Richard James, Norman Macmillan, Peter Carpenter, Richard Jeffries Dawes, Norman Cyril Jones, Ernest Masters, Henry Moody, Thomas F. Williams, William Wright, James Dewhirst, James Belgrave, Edward Clarke, Alfred Haines, Thomas M. Harries, Alan Rice-Oxley, Earl Hand, Arthur Harris, Charles Gray Catto, John Pinder,[3] and future Group Captain Sidney Cottle.

[6] The following day, the squadron participated in an attack on shipping at Tobruk, damaging the Italian cruiser San Giorgio.

[7] During late 1940 the squadron supported Allied ground forces in the East African Campaign, while based at Gura, in Eritrea.

[9] Between June and August 1941, the squadron was based at RAF Aqir in Palestine, from where it was involved in operations against Vichy French forces in Lebanon.

The unit also engaged in operations to quell unrest on the Sarawak coast in British North Borneo during this time period.

[2] On 1 August 1972, the squadron was reformed at RAF West Raynham, equipped with Hawker Hunter FGA.9s, as a ground-attack training unit.

As a 'Shadow Squadron' or war reserve, the squadron's war role was as a fully operational unit composed mainly of instructors, and assigned strike and other duties by SACEUR in support of land forces on the Continent resisting a Soviet assault on Western Europe, by striking at targets assigned by SACEUR, beyond the forward edge of the battlefield, deep within enemy-held areas, first with conventional weapons and later with tactical nuclear weapons if a conflict escalated to that level.

45(R) Squadron moved to RAF Cranwell in October 1995, and in 2003, replaced its BAe Jetstream T.1s with Beechcraft B200 King Airs serviced by Serco.