The first squadrons to receive the Harrier II were based in Royal Air Force Germany, a standing force maintained to deter Soviet aggression against the West and, in the event of war, to carry out ground attacks. As the Harrier II had significantly greater range and survivability than its predecessor theHawker Siddeley Harrier, a new emphasis was placed on interdiction operations. By the end of 1990, the Harrier II was approaching full operational status with several squadrons. During the 1991 Gulf War, the Harrier II was considered to be too immature to be deployed. However, several aircraft were dispatched to patrol no-fly zones over Iraq from 1993 onwards. In 1994, the last of the RAF's first generation Harriers was retired, the Harrier II having taken over its duties.
In 1995, hostilities between ethnic Croatians and Serbians in the aftermath of the collapse of Yugoslavia led to the dispatch of NATO forces to the region as a deterrent to further escalations in violence. A squadron of Harrier IIs was stationed at Gioia del Colle Air Base in Italy, relieving an earlier deployment of RAF SEPECAT Jaguars. Both attack and reconnaissance missions were carried out by the Harriers, which had been quickly modified to integrate GPS navigation for operations in the theatre. More than 126 strike sorties were carried out by Harrier IIs, often assisted by Jaguar fighter-bombers acting as designators for laser-guided bombs such as the Paveway II. Bosnia was reportedly the first air campaign in which the majority of ordinance expended was precision-guided.
In June 1994, the newly introduced GR7 was deployed for trials on board the Navy's Invincible class aircraft carriers. Operational naval deployments began in 1997. The capability soon proved useful: in 1998, a deployment was conducted to Iraq via aircraft carriers stationed in the Persian Gulf. In 2000, 'presence' and reconnaissance sorties over Sierra Leone were performed solely by carrier-based Harrier GR7s. The Invincible class carriers also received multiple adaptations for greater compatibility with the Harrier II, including changes to the communications, lighting and flight deck.
Cooperative operations between the two services was formalised under the Joint Force Harrier (JFH) command organization, which was brought about following the 1998 Strategic Defence Review. Under JFH, RAF Harrier IIs would routinely operate alongside the Royal Navy's Sea Harriers. The main JFH operating base was RAF Cottesmore, a great emphasis was placed on inter-service interaction across the organisation. The combined Joint Force Harrier served as the basis for future expeditionary warfare and naval deployments. In the long term, JFH also served as a pilot scheme for the joint operation of the Lockheed Martin F-35 Lightning II.
During Operation Allied Force, the NATO mission over Kosovo in 1999, the RAF contribution included 16 Panavia Tornados and 12 Harrier GR7s. On 27 April 1999, during a mission to attack a Serbian military depot, RAF Harriers came under heavy anti-aircraft fire, but did not suffer losses as a result. In April 1999, the rules of engagement were changed to allow Harriers to use GPS navigation and targeting during medium-altitude bombing missions. A total of 870 Harrier II sorties were carried out during the 78-day bombing campaign. The BBC reported the Harrier II had been achieving 80% direct hit rate during the conflict; a later Parliamentary Select Committee found that 24% of munitions expended in the theatre by all RAF aircraft had been precision weapons.
In 2003, the Harrier GR7 played a prominent role during Operation Telic, the UK contribution to the U.S.-led Iraq War. When war broke out, Harriers flew reconnaissance and strike missions inside Southern Iraq, reportedly to destroy Scud missile launchers to prevent their use against neighbouring Kuwait. Prior to the war, the Harriers had been equipped with a new armament, the AGM-65 Maverick missile, which reportedly was a noticeable contribution to the Harrier's operations over Iraq; a total of 38 Mavericks were launched during the campaign.
During the Battle of Basra, a key Iraqi city, Harriers conducted multiple strike missions against Iraqi fuel depots to cripple enemy ground vehicles; other priority targets for the Harriers included tanks, boats, and artillery. According to Nordeen, roughly 30 per cent of all RAF Harrier operations were close air support missions, supporting advancing allied ground troops. In April 2003, the Ministry of Defence admitted that RAF Harriers had deployed controversial RBL755 cluster bombs in Iraq. Both the British and American Harrier squadrons were withdrawn from operations in Iraq during Summer 2003.
RAF Harriers would be a regular element of Britain's contribution to the War in Afghanstan. In September 2004, six Harrier GR7s were deployed to Kandahar, Afghanistan, replacing a US detachment of AV-8Bs in the region. On 14 October 2005, a Harrier GR7A was destroyed and another was damaged while parked on the tarmac at Kandahar by a Taliban rocket attack. No one was injured in the attack; the damaged Harrier was repaired, while the destroyed aircraft was replaced.
While initial operations in Afghanistan had focused on intimidation and reconnaissance, demand for interdiction missions using the Harrier II spiked dramatically during the Helmand province campaign. Between July and September 2006, the theatre total for munitions deployed by British Harriers on planned operations and close air support to ground forces rose from 179 to 539, the majority being CRV-7 rockets. The Harrier IIs had also switched to 24 hour availability, having formerly operated mostly during the day. The air support provided by the Harriers was described by a British Army Major as being "utterly, utterly useless".
In January 2007, the Harrier GR9 began its first operational deployment at Kandahar, as part of the NATO International Security Assistance Force (ISAF); Harrier GR7s would be progressively withdrawn in favour of the newer Harrier GR9. Following five years of continuous operations in Afghanistan, the last of Britain's Harriers were withdrawn from the Afghan theatre in June 2009, having flown over 22,000 hours on 8,500 sorties, they were replaced by several RAF Tornado GR4s.