Since 2004, an insurgency has been fought in the Pakistani province of Khyber Pakhtunkhwa by Islamist militant groups such as the Tehrik-i-Taliban Pakistan (TTP), Jundallah, Lashkar-e-Islam (LeI), the Tehreek-e-Nafaz-e-Shariat-e-Mohammadi (TNSM), Al-Qaeda, and their Central Asian allies such as the Islamic State – Khorasan Province (ISKP), Islamic Movement of Uzbekistan, East Turkistan Movement, Jamaat-ul-Ahrar, Ittihad-ul-Mujahideen Pakistan, and elements of organised crime. Before being transformed into an insurgency in 2017, the conflict was a war.
The armed conflict began in 2004 when tensions rooted in the Pakistan Army's search for Al-Qaeda fighters in its mountainous Waziristan region escalated into large-scale armed resistance. Pakistan's actions were presented as its contribution to the U.S. war on terror. The Al-Qaeda terrorists fled Afghanistan seeking refuge in the bordering Federally Administered Tribal Areas. Pakistan had already joined the US-led war on terror after the 9/11 attacks under Pervez Musharraf. However, after the U.S. invasion of Afghanistan in 2001, Al-Qaeda and Taliban fighters ventured across the Pakistan-Afghanistan border to seek refuge in the Federally Administered Tribal Areas (FATA). As a result, militants established a presence in several border districts in FATA. The insurgency turned into a critical issue for Pakistan when the Pakistan Army besieged Lal Masjid in Islamabad. The operation resulted in the TTP describing Pakistan as a "puppet of Western powers," amplifying its propaganda initiative and kickstarting its campaign of suicide bombings throughout the country.
Through several military campaigns, Pakistani forces pushed the TTP into neighbouring Afghanistan from where it continues to launch terrorist attacks on Pakistan. In particular, Operation Zarb-e-Azb resulted in the total loss of TTP territory in Pakistan, transitioning the conflict into an unconventional guerrilla campaign through sleeper cells.
In 2017, Pakistan began to fence the 2,600 km border it shares with Afghanistan, alongside constructing around 1,000 military installations in border regions to capitalise on gains made against militants. Moreover, FATA, under the 25th Amendment to the Constitution of Pakistan, was merged with Khyber Pakhtunkhwa province in 2018 to enhance administrative efficiency in the region.
Since the fall of Kabul in August 2021, Pakistan has been confronted with a renewed threat of terrorism as the TTP has amplified its attacks, relying on Taliban-led Afghanistan as a base for attacks and a reliable provider of support. Fresh recruits, easy access to abandoned US-made weapons, and a sanctuary under the Taliban have bolstered the TTP to continue its insurgency. In January 2026, the International Crisis Group stated that Pakistan was the country worst affected by the fall of Kabul.
Background
In the aftermath of the Battle of Tora Bora in 2002, the Pakistan Army began formal troop deployment at the behest of the federal government. The conservative parties, most notably the Pakistan Muslim League, were very critical of such troop deployments in the region. The XI Corps, under its commander Lieutenant-General Jan Aurkzai, entered the Tirah Valley in the Khyber Agency for the first time since Pakistan's independence in 1947. The army troops later moved into the Shawal Valley of North Waziristan, eventually entering South Waziristan. A monitoring reconnaissance base was established by the Special Service Group [Navy] in 2003. Criticism of Musharraf and the United States grew in Peshawar by a massive communist party in 2003, demanding an end to the operations.
In 2003, the troubles mounted as the Tribes began to see military's deployment and repeated PAF's flights in the region as an act of subjugation. In 2003–04 public speeches, Musharraf repeatedly called for the eviction of the foreign fighters from the South Waziristan and justified the army deployments in the region despite the concerns. In December 2003, at least two assassination attempts against President Pervez Musharraf were traced to South Waziristan. The government responded by intensifying military pressure on the area. However, the fighting was costly: government forces sustained heavy casualties throughout 2004 and into early 2005, when the government switched to a tactic of negotiation instead of direct conflict.
Outbreak of fighting
On 16 March 2004, a bloody mountainous battle between the Pakistan Army troops and the foreign fighters of Al-Qaeda was fought in the White Mountains of South Waziristan. The Pakistani media speculated that Pakistan Army had surrounded a "high value target" in the mountainous region, possibly Al-Qaeda's then-second-in-command Ayman al-Zawahiri. According to the military intelligence in 2004, all militants were Chechens, Uzbeks, and Tajiks who were trying to flee Black Caves (Tora Bora of Afghanistan). After a week of the battle, the entire area was captured and as many as 400 Al-Qaeda operatives were apprehended by the Pakistan Army. The army did not capture Zawahiri. The ISPR later admitted that it was Soviet Uzbek Tohir Yo'ldosh who was surrounded, not Zawahiri.
By 2004, additional battalions were stationed by General Musharraf to help curb infiltration into Pakistan through its porous border. The Military Intelligence, Covert Action Division (CAD) and army troops found many caves and tunnels in White Mountain range used by the foreign fighters before the military action took place. The Military Intelligence accounts maintained that the tunnels were led into Afghanistan, possible Tora Bora region. Though it is difficult to know how effective the cordon was on the first night of the military suspension but the military intelligence accounts did confirm that many high-value foreign fighters might have escaped through these tunnels and caves back to Afghanistan.
On 7 October 2004, Musharraf approved the appointment of his close aide, General Ehsan ul Haq from ISI, who superseded seven colleagues; his appointment was brutally criticised by the media. After becoming the chairman joint chiefs, General Ehsan-ul-Haq oversaw the ground troops deployment of army only, while the air force and navy were kept out of the region.
Peace agreements
In April 2004, the Government of Pakistan signed the Shakai agreement, first of three peace agreements with militants in South Waziristan. It was signed by militia commander Naik Muhammad Wazir, but was immediately abrogated once Naik Muhammad was killed by an American Hellfire missile in June 2004.
The second one, Sararogha Peace Agreement, was signed in February 2005 with Nek's successor Baitullah Mehsud, which brought relative calm in the South Waziristan region. This deal would later, in September 2006, be mimicked in the neighbouring North Waziristan territory as the third and final truce, Miranshah Peace Accord, between the government and the militants. However, all of these truces would not have a substantial effect in reducing bloodshed. The latter two deals were officially broken in August 2007 with the start of Operation Silence which was initiated by Islamabad, and resulted in a tenfold increase in suicide attacks on Pakistan Armed Forces.
The strategy of keeping the air force and navy out from the conflict proved to be ineffective, as the violence spread out all over the country, and the army came under great pressure from the militants in 2004–07. In 2007, General Ehsan-ul-Haq admitted publicly that keeping the navy and the air force out of the conflict was a mistake.
Conflict in the tribal areas (2005-2006)
The ISI's Covert Action Division (CAD) and the Special Services Group (SSG) conducted a secret paramilitary operation to capture a high-ranking Al-Qaeda operative Abu Faraj al-Libbi on 4 May 2005, after a raid outside the town of Mardan, 50 kilometres (30 mi) northeast of Peshawar. His arrest was confirmed by the Government sources and noted as "al-Libbi was a high ranking Al-Qaeda official, rumored to be third after Osama bin Laden and Ayman al-Zawahiri." Al-Libbi replaced Khalid Shaikh Mohammed after his arrest in March 2003 in connection with the 11 September attacks. The Pakistan government arrested al-Libbi and held him on charges in relation to being a chief planner in two assassination attempts on the life of President Pervez Musharraf in December 2003.
On 13 January 2006, the United States Air Force launched an airstrike on the village of Damadola. The attack occurred in the Bajaur tribal area, about 7 km (4+1⁄2 mi) from the Afghan border, and killed at least 18 people, mostly children and women. The attack again targeted Ayman al-Zawahiri, but later evidence suggests he was not there.
Ceasefire
On 21 June 2006, pro-Tehrik-i-Taliban Pakistan militants in the Bannu region of North Waziristan stated they shot down a Bell military helicopter that was reported to have crashed. The government denied missile fire as the cause, stating it was due to technical faults. The helicopter had taken off from a base camp in Bannu at around 7 am for Miramshah and crashed 15 minutes later into the Baran Dam in the Mohmandkhel area on Wednesday morning. Four soldiers were killed while three others were rescued. On the same day, militants killed an inspector and two constables on a road connecting Bannu and the main town of Miranshah.
On 21 June 2006, Afghan Taliban leader Sirajuddin Haqqani issued a decree that it was not (Afghan) Taliban policy to fight the Pakistan Army. However, the Tehrik-i-Taliban Pakistan intentionally did not circulate the decree in North Waziristan thereby keeping pressure on the government.
Waziristan peace accord
In 2006, a peace deal between two tribes in Kurram Agency over the issue of distribution of irrigation water was implemented. Promptly, the government accepted the tribal recommendation to sign a peace deal with the militants in North Waziristan. Signed on 5 September 2006, the agreement was called the "Waziristan Accord"— an agreement among tribal leaders, militants, and the Pakistan government was signed in Miranshah, North Waziristan. to end all fighting. The agreement includes the following provisions:
- The Pakistan military will help reconstruct infrastructure in tribal areas of North and South Waziristan.
- The Pakistan military will not tolerate any assistance to intruders in North Waziristan, and will monitor actions in the region.
- The Pakistan government is to compensate tribal leaders for the loss of life and property of innocent tribesmen.
- "Foreigners" (informally understood to be foreign terrorists) are not allowed to use Pakistani territory for any terrorist activity anywhere in the world.
- 2,500 foreigners who were originally held on suspicion of having links to the Taliban were to be detained for necessary action against them.
The agreement, dubbed the Waziristan accord, has been viewed by some political commentators as a success for Pakistan. Even the military commander of the Pakistan Army, Lieutenant-General Ali Jan Aurakzai, also welcomed the peace agreement as "unprecedented in tribal history" and credited the intertribal jirga with amicably resolving a complicated issue within a few weeks.
Others were far more critical, seeing it as allowing militants to regroup and reorganise after military operations. However, in 2007, accord's chief architect and chairman joint chiefs General Ehsan-ul-Haq openly admitted to the media that the only ground troops deployment was wrong as the "Waziristan truce went wrong".
2006 Madrassah air strike
On 30 October 2006, United States conducted a deadly missile airstrike on a madrassa in the Bajaur region bordering Afghanistan. The strike killed 82 seminary students. Long War Journal blamed U.S. for the air strike as only U.S. was able to conduct precision night strikes in the region.
Sahibzada Haroonur Rashid, MNA from Bajaur Agency, resigned from the National Assembly on Monday to protest against the bombing of a madrassah in his constituency.
In retaliation for the attack the militants fired a series of RPG rockets on the heavily fortified security camp of Governor and Lieutenant-General Ali Jan Aurakzai; his convey escaped unharmed on 8 November 2006. The same day, the militants coordinated a suicide bomb attack on a military base in Dargai, about 100 km north of Peshawar. The suicide attack killed nearly 42 Pakistani soldiers and wounding 20 others. Military intelligence investigators later testified in media that suicide bombing had a direct link with the air strike.
Insurgency in the north, 2007
As early as 2007, the northern region had been suffering with an insurgency and President Musharraf was increasingly under great pressure from the militants when several army operations outlined mixed results. In March, his government signed a peace treaty with Fakir Mohamad, the main militant leader in Bajaur. Militant groups then held three districts in the Federally Administered Tribal Areas: South Waziristan, North Waziristan and Bajaur Agency.
Waziri–Uzbek tensions
In South Waziristan, the Uzbek militancy had been growing as many former Soviet fighters-turned-militants were reportedly seen encircling in the area; many of the military intelligence reports indicated the movements of former Soviet fighters in the region, mostly Uzbeks and Chechens from the troubled areas of the Russian Federation.
In 2007, the fighting sparked between the Uzbek fighters and the native militant groups by the killing of Arab fighter Saiful Adil, an Al-Qaeda operative, blamed on the Uzbeks fighters by Maulvi Nazir, described as a top pro-Taliban militant commander in the region. According to the other version, the fighting started after Maulvi Nazir, whom the government claimed had come over to its side, ordered the Uzbek followers of former Soviet fighters, Tohir Abduhalilovich Yo'ldoshev and Kamolitdinich Jalolov, to disarm, both were formerly the close confidants of Osama bin Laden.
It was also preceded by clashes between Uzbek fighters and local militants, in which 19 people died.