Allies In War, Enemies In Peace: The Unraveling Of Pakistan–Taliban Relations

Once close partners against the U.S. occupation, Pakistan and Afghanistan’s Taliban government now trade accusations of betrayal, revealing deeper crises of mistrust, militarism, and faith across the Muslim world’s most volatile border.

October 2025

Strained Relations Four Years After Taliban Takeover

Four years after a Taliban conquest of Afghanistan widely welcomed in Pakistan, relations between the two neighbors have struck a low as each accuses the other of supporting its insurgency, reaching a nadir this week with skirmishes on the border.

Taliban soldiers

Where the Taliban emirate accused Pakistan of supporting a Daesh underground, Pakistan’s military-led coalition regime has accused Afghanistan of supporting insurgents, including a namesake insurgency in northwest Pakistan’s Pashtun borderland. The more pressing insurgency in Pakistan stems neither from Afghan malfeasance, as Islamabad claims, nor is it an entirely domestic affair, as Kabul counters.

Buried among the rhetoric, blame-trading, and saber-rattling are several inconvenient truths that neither regime nor its cheerleaders seems inclined to acknowledge, but which are critical to factor into any solution.

Contrasting Claims and Misrepresentations

Pakistani accusers rightly note that insurgent leaders Nur-Wali Asim of the Mahsud clan and Gul Bahadur of the Wazir clan have received refuge in Afghanistan, and that attacks picked up pace since the Taliban return to Kabul in 2021. Afghan rejoinders rightly point out that the roots of Pakistan’s crisis are domestic and largely self-inflicted: a consistently militaristic policy in the borderland has failed for years regardless of insurgent leaders’ whereabouts, while none of Afghanistan’s other neighbors have faced such a problem despite their own insurgents’ “refuge” in the emirate.

The most extreme claims on either side resort to obfuscation. On one hand are exaggerated Taliban claims of Pakistani complicity in the American occupation of Afghanistan, which ignore the greater role of other states —especially Pakistan’s archrival India, a cheerleader of the occupation right to and beyond its end— and the respite that successive Pakistani regimes gave despite considerable American irritation. On the other hand are nationalistic claims, especially loud among supporters of the Pakistani military, that claim primordial Afghan hatred, conspiracy, and ingratitude.

Historical Ironies and Shifting Allegiances

The latter claim contributed to an atmosphere where thousands of Afghans have been callously and humiliatingly uprooted from decades-long refuge. Ironically, this claim is itself a misdirected rejoinder to longstanding claims by the preceding, American-installed government of Afghanistan, which claimed in ethnicized terms that the Taliban were merely a cat’s paw of scheming “Punjabi” Pakistanis. By painting opponents as Pakistani puppets, the Afghan regimes of 2001–21 disingenuously portrayed their own utter dependency on a foreign invasion as a sort of nationalist virtue against their neighbor’s meddling.

The claim that Pakistan’s insurgency has accelerated since 2021 misses the point that for much of the prior fifteen years, its deceleration had been assisted through Taliban mediation, which persuaded many such militants to help fight the United States in Afghanistan rather than fight the Pakistani government. This stance was particularly emphasized by the Haqqanis, who have had a decades-long policy of support for Pakistan as far afield as Kashmir.

Nor was it an exclusively Taliban stance: in 2004–05, Pakistani corps commander Safdar Hussain, who led the first campaigns in northwest Pakistan against Wazir and Mahsud insurgents, urged them to abandon revolt against Islamabad and focus on jihad against the Americans. An unamused United States repeatedly attacked deals between the military and the insurgents; for example, Sirajuddin Haqqani mediated at Miranshah between Bahadur and the military in 2006, only for American airstrikes to sabotage the agreement.

The Rise of New Militants

Qari Saifullah Akhtar

This prompted a number of Pakistani militants to disavow the Pakistani regime and take up arms. Many were longstanding fighters who felt betrayed by the state that had once backed them, and ignored the pleas of such scholars as the Usmani brothers, Muftis Taqi and Rafi, to stand down.

One such militant was Saifullah Akhtar, whom Rafi had known in the 1980s and complimented in a subsequent 1990s book that also saluted the Taliban movement; his newfound hostility to a regime within whose military he had significant contacts was particularly dangerous, yet he was eventually persuaded to leave Pakistan and fight alongside the Taliban in Afghanistan, where he was killed.

A Balancing Act Between Foes and Allies

The modus vivendi that the Taliban adopted was to maintain ties with both sides of the Pakistan war, the army and the insurgency, in a manner similar to how the Pakistani military kept links with both sides of the Afghan war, the United States and the Taliban. Rejecting insurgency against Pakistan, on numerous occasions, Taliban mediation redirected Pakistani insurgents against the United States.

A number of secondary Taliban commanders did sympathize with the Pakistani insurgency against a state they saw as having betrayed them: a sentiment that no doubt retains currency in the rank-and-file. But this was always an informal minority: Sirajuddin, whose uncles Khalilur-Rahman Ahmad and Ibrahim Umari played a key role in coordination with Pakistani officers, also urged such Pakistani counterparts as Bahadur to focus their attention on the Americans in Afghanistan.

This preceded a major turning point in 2014, during a major campaign by the Pakistani army, yet this success relied in part on also internecine disputes among the insurgents after the elimination of a series of leaders.

A major factor was the emergence of Daesh, to which large parts of the insurgency defected. Although it opposed both rival governments in Islamabad and Kabul, Daesh’s principal target was the Taliban, whom it accused of inauthenticity and—ironically given today’s circumstances—servitude to Pakistan. The conflict with Daesh forced the Taliban to draw closer to Pakistani insurgents, such as Bahadur and Mahsud preacher Nur-Wali Asim, as a counterweight.

Reform Efforts Under Imran Khan

Imran Khan

A major factor in draining the insurgency was the major attempts at reform made by Imran Khan’s Insaf Party, which assumed Khyber-Pakhtunkhwa’s provincial government. Khan had drawn support in large part from his opposition to the American “war on terror” and Pakistani acquiescence therein: by all accounts, the Insaf government in Khyber-Pakhtunkhwa was a major improvement, and retains major support in the province to this day.

It also tried to incorporate the historically autonomous, but increasingly militarized, Waziristan borderland under its control, which Nur-Wali opposed as this approach promised to solve many of the grievances on which he drew.

Nur-Wali’s Hardline Stance

Though Nur-Wali reorganized the insurgency and, to an extent, its conduct, he refused to negotiate, painting his fight as part of a historical Mahsud resistance against British colonialism and a Pakistani state seen as its American-backed heir. In fact, the Mahsuds who fiercely fought Britain had largely supported Pakistan right up to the 2004 incursion in Waziristan—a product not of primordial Pakistani illegitimacy but rather involvement in the much more recent American war on terror. This stance was far harsher than that of the Taliban and even affiliated insurgents like Bahadur, and has precluded meaningful negotiations.

Insurgencies and Unneighborly Behavior

The Pakistani claim that the Taliban’s return to power in 2021 coincided with a sharp uptick in attacks within Pakistan ignores the fact that the previous decade’s decline owed in part to repeated Taliban mediation on Islamabad’s behalf. On the other hand, as I pointed out at the time, Taliban wariness of Daesh meant that they cultivated ties with Pakistani insurgents: famously, upon capturing Kabul, they executed Daesh leader Ziaul-Haq Zia but released the Pakistani insurgent leader Faqir Mohammad.

Yet this was not an inherently anti-Pakistan move: Faqir had been imprisoned by the previous Afghan regime precisely because he was seen as more amenable to negotiations with Islamabad, and Sirajuddin Haqqani, now Taliban interior minister, immediately held negotiations between Imran’s Pakistani government, including the military represented by spymaster Faiz Hameed, and militants like Bahadur.

Post-Imran Escalation and Missteps

Whether this would have succeeded is unknown—certainly some militants continued to snipe away at Pakistan regardless and might have never reconciled—but the 2022 coup that ousted Imran, and quickly courted relations with an anti-Taliban United States, escalating not through targeting insurgent units in Pakistan but bombing across the Afghan border—the sort of unilateral action that was bound to raise Taliban hackles. The Pakistani military, led by Asim Munir, has made a point of theatrical escalation with Kabul—yet its initial focus was not the Pakistani insurgency, which gained ground over 2023, but crushing Imran’s still-influential party through major, occasionally bloody, suppression and electoral manipulation.

Deportations and Counterproductive Policy

The response toward the insurgency has similarly been unimpressive and counterproductive to its stated aims, particularly the mass deportation of Afghans that began in autumn 2023. This was a political decision that aimed to give the impression of vigilance by whipping up anti-Afghan sentiments; in its rivalry with the Insaf party, the military establishment and its many hangers-on have portrayed both Taliban and Afghans broadly as scheming confederates of Imran in a sort of fifth column. This provoked widespread hostility among affected communities in the borderland.

It was also practically counterproductive: the mass deportations of Afghans across the border logistically confounded the task that Pakistan demanded of the Taliban, to intercept Pakistani insurgents. This was further complicated by the fact that Daesh remained an underground threat, assassinating many Taliban officials, fighters, and leaders, including Sirajuddin’s uncle Khalilur-Rahman, governor-general Daud Muzamil, and corps commander Hamdullah Mukhlis. With their own challenges, the Taliban are hardly in a position to solve Pakistan’s largely self-inflicted woes.

Half-Hearted Cooperation and Growing Misgivings

This does not, however, remove the fact that Taliban cooperation has been at best half-hearted. In part, this stems from its reluctance to alienate non-Daesh militants, who have, in fact, flared up in indignation whenever the emirate has tried to relocate them away from the Pakistani border. In part, it stems from misgivings toward a confrontational Pakistani military bent on scapegoating Afghanistan for all internal challenges. It also stems from an insistence that the Pakistani insurgency is a primarily internal issue: after all, the Taliban also hosts opposition militants from other countries, none of which have caused anywhere near the amount of trouble as the Pakistani insurgents. To this extent, the argument made by both Khan and the Taliban that the Pakistani insurgency stems from internal Pakistani grievances holds truth.

Parallel Rejections and Border Tensions

Yet if the Pakistani military has been aggressive, Taliban denials ring irrelevant if not hollow. The indignation the emirate evinced when Islamabad flirted with exiled critics is hardly more than that in Pakistan when it sees the likes of Nur-Wali given deferential treatment in Afghanistan. The rejectionism that Nur-Wali directs toward Islamabad is similar to that which Daesh directs toward Kabul. No state, Pakistan or others, tolerates repeated cross-border raids of the type the Taliban are unwilling to interdict for reasons more of political expediency than principle.

Structural Causes and Continuing Violence

On the other hand, the emirate’s ability to control the border has been severely circumscribed by such clumsy and destructive policies as the mass deportations of Afghans. The Taliban spent over a decade, even while fighting a guerrilla war against the United States, mediating with the Pakistani insurgency on behalf of the same military that now scapegoats it.

The Pakistani war is not a product of Taliban inaction: even if the Taliban surrendered every Pakistani insurgent leader from Afghan territory, the twenty-year militarization, social upheaval, and political disputes that exacerbated the war remain. Some twenty senior insurgent leaders have been killed, almost on a yearly basis, since the Waziristan conflict broke out in the mid-2000s, and there is little reason to suppose that the capture or killing of Nur-Wali or Bahadur would make a long-term difference without addressing issues in an approach that the military of late has flatly shunned. Bombing Kabul in pursuit of Nur-Wali might give some short-term catharsis and a few bragging rights, but it only threatens to exacerbate mistrust without addressing these underlying issues.

When these obvious points are raised, however, a military increasingly intolerant of contradiction lashes out.

Forward Steps and Barriers

The solution is not as complicated as it might seem. Both Pakistan and Afghanistan’s insurgents stem from the same geographic stretch, the border highlands, which both states have long struggled to control. The simplest task is, in military terms, joint security collaboration against both Afghan and Pakistani insurgents, and in sociopolitical terms, an improved and more accountable governance. A sensible policy would see Afghanistan and Pakistan cooperate on this region rather than trade mostly spurious accusations and recriminations.

The barrier to such commonsense is the exponential mutual mistrust, related to the two neighbors’ addiction to alliances that have only ever escalated the problem—for Taliban with Pakistani insurgents who are airily whitewashed as “good Muslims” regardless of the number of Muslims their war victimizes; and for Pakistan’s military with a United States that it has shamelessly courted since 2022, partly pursuant to its feud with Imran, regardless of the sociopolitical costs it brings to the country.

It is easier to scapegoat a neighbor through selectively remembered or distorted history rather than introspect and apply to them the same standards sought in one’s own country: so much for Muslim neighbors in the “Islamic emirate” and the “Islamic nuclear power.”

Related:

On the Pakistan-India Dangerous Escalation

Afghanistan’s Experiment: Progress and Peril Under Taliban Rule