Pakistan-Afghanistan: A Strained Relationship on the Brink

Mujahideen, the Taliban, and an uncertain future

Credit: Shutterstock.com/RobNaw

Pakistan-Afghanistan: A Strained Relationship on the Brink

In 2024, Pakistan witnessed its deadliest year in nearly a decade, with over 3,000 people killed in terrorist attacks. The majority of these attacks were attributed to Tehrik-e-Taliban Pakistan (TTP), a militant group based in Pakistan’s northwestern tribal regions but accused of using Afghan territory for refuge. Tensions reached a boiling point in December 2024 when Pakistan launched airstrikes inside Afghanistan, targeting alleged TTP hideouts. With continuing border skirmishes, Afghanistan’s growing ties with India, and Pakistan’s ongoing security crisis, it is difficult to predict where the Pakistan-Afghanistan relationship will be at the end of this year.

From Mujahideen to Taliban: Pakistan’s Afghan Strategy

Pakistan’s active involvement in Afghanistan dates back to the 1980s Soviet-Afghan War when it became a key patronizer of the Afghan Mujahideen fighting Soviet forces. The Taliban later emerged from one of these Mujahideen factions. The Taliban later emerged from one of these Mujahideen factions. With U.S. and Saudi backing, Pakistan’s Inter-Services Intelligence (ISI) trained and armed Mujahideen fighters, contributing to the Soviet withdrawal in 1989 after nearly a decade of conflict.

However, post-war Mujahideen factions descended Afghanistan into a civil war, which lasted more than a decade, till the end of the last century. The Taliban emerged in 1994, named after the Pashto word for ‘students,’ as many of its early members were Pashtun students.

Within two years, the Taliban captured Kabul and established the Islamic Emirate of Afghanistan. Though Pakistan denies any involvement, reports suggest ISI patronized the Taliban to secure influence. Pakistan was also one of only three countries to recognize the Taliban government in the 1990s.

Following 9/11, Pakistan’s alliance with the U.S. brought a massive aid windfall but also severely strained its ties with the Taliban. As Pakistan provided logistical support for the U.S.-led War on Terror, many pro-Taliban Islamist groups became increasingly radicalized, leading to the rise of large-scale terrorism in Pakistan for the first time.

After the U.S. withdrawal from Afghanistan in 2021, Pakistan hoped for improved relations with the Taliban. However, tensions escalated over various conflicting issues.

Enduring Disputes in Pak-Afghan Relations

For decades, Pakistan and Afghanistan have remained entangled in disputes over territory, water resources, and refugee issues.

The Pakistan-Afghanistan border, known as the Durand Line, was drawn in 1893 and remains the most contentious issue. While Pakistan insists it is an internationally recognized boundary Afghanistan refuses it, arguing it was a colonial-era imposition and expired with British rule. Islamabad supported the Taliban during the Afghan civil war, hoping for their recognition of the Durand Line, but to this day, the Taliban dismisses it as a “hypothetical line.” The border also divides Pashtun communities, creating lasting resentment over their forced separation.

An anonymous Pakistani third-year Georgetown student from a Pashtun background, describes the impact: “Our families live just a short distance apart on both sides of the border, yet we cannot visit them without a permit. Recently, the process has become even more restrictive.”

Beyond territorial disputes, water rights and migration issues add to tensions. The Kabul River flows from Afghanistan into Pakistan, vital for 20 million people. Afghan dam projects like the Shahtoot Dam have raised concerns over reduced downstream water flow, exacerbating tensions without a formal water-sharing agreement.

Meanwhile, the Afghan refugee crisis remains a point of contention. Pakistan has hosted millions of Afghan refugees, with 1.35 million still registered. However, citing economic and security concerns, Islamabad intensified crackdowns on undocumented refugees in late 2023, arguing they should return post-war. The Taliban strongly opposed the move, calling it ‘unacceptable behavior’, further straining ties.

The Rise of TTP and Pakistan's Security Fallout

While historical disputes continue to strain relations, it is the resurgence of Tehrik-e-Taliban Pakistan (TTP) and escalating militancy that have pushed Pakistan and Afghanistan into the most recent confrontations.

The U.S.-led invasion of Afghanistan in 2001 forced many Taliban fighters into Pakistan, seeking refuge in rugged border regions where difficult terrain and strong Pashtun tribal networks made it nearly impossible for Pakistani authorities to control the influx. The U.S. launched drone strikes targeting Taliban fighters, which often resulted in civilian casualties, fueling resentment and further strengthening support for the Taliban.

Amid this instability, several Islamist militant factions emerged, viewing Pakistan as a U.S. ally complicit in their persecution. In 2007, these groups merged to form the Tehrik-e-Taliban Pakistan (TTP), also known as the Pakistan Taliban, aiming to impose strict Sharia law and overthrow the Pakistan government.

The Pakistani Georgetown student, reflecting on the TTP’s rise, said:

“Since Pakistan’s creation, radical Islamists existed among the Pashtun population, but in small numbers with little public support. Today, they are our biggest domestic threat.”

Since its formation, the TTP’s terrorist attacks have targeted both military personnel and civilians, resulting in thousands of deaths. The most devastating attack occurred in December 2014, when TTP gunmen stormed a school in the Pashtun majority province’s capital Peshawar, and massacred 130 schoolchildren marking the deadliest terrorist attack in Pakistan’s history.

Pakistan’s Miscalculated Taliban Strategy

Believing that a Taliban-led Afghanistan would help contain the TTP, Pakistan under Imran Khan’s premiership (2018-2022) actively supported the Taliban’s return to power. His government repeatedly framed the U.S. involvement in Afghanistan as a foreign intervention, and when the Taliban seized Kabul in August 2021, Khan hailed it as “breaking the shackles of slavery.”

However, Pakistan’s expectations quickly unraveled. They alleged that the Taliban government provides TTP with safe hideouts inside Afghanistan. Kabul always denied such claims. Pakistan tried negotiating with the TTP in 2022, but the talks collapsed.

Since then, attacks by TTP have increased on an unprecedented scale. In 2024 alone, Pakistan lost 3,000 lives, including 2,546 civilians in terrorist attacks, making it the deadliest year for Pakistan in a decade. Most of the attacks were perpetrated by the TTP.

Pakistan’s military operations have proved ineffective against TTP militants, who, according to Islamabad, easily flee to Afghanistan. To curb cross-border militancy, Pakistan has attempted to fortify the border by constructing a fence along the Durand Line, but the Taliban strongly opposes this effort.

On Dec. 21, 2024, TTP militants stormed a Pakistani security outpost, killing 16 soldiers. On Dec. 25, Pakistan responded with cross-border airstrikes in Afghanistan’s Patakia district, reportedly killing at least 46 people, including civilians.

While Pakistan claimed the targets were TTP hideouts, the Taliban government stridently denied and promised to retaliate. Three days later, they claimed to attack Pakistani military installments but few details were disclosed.

TTP, Taliban, and Pakistan: A Fragile Standoff

The Taliban’s reluctance to take action against the TTP is a result of a complex reality. Experts argue that any move against TTP could fracture Taliban unity and allow more extremist groups like Islamic State Khorasan Province (ISKP) to expand. The Taliban’s stance mirrors Pakistan’s past strategy, where Islamabad dismissed Afghan and U.S. demands to curb Taliban activities within Pakistani borders.

For Pakistan, airstrikes inside Afghanistan serve multiple objectives—dissuading TTP operations, signaling strength to the domestic audience, and giving the Afghan Taliban a strong message that they would not hesitate to cross the border. However, continued military action risks deepening anti-Pakistani sentiments among Afghans and further alienating Pakistani Pashtuns.

The Uncertain Future

Since the December 2024 airstrikes, Pakistan-Afghanistan relations have sharply deteriorated. Notably, on the same day Pakistan launched the strikes, a Pakistani diplomatic envoy was in Kabul for negotiations. The Taliban condemned the attack as a violation of Afghan sovereignty, stating that conducting airstrikes while engaging in diplomatic talks reflected Pakistan’s insincerity in resolving the issue.

Tensions have further escalated in early 2025, with increased border skirmishes between Afghan and Pakistani forces. Their busiest Torkham border crossing has been closed since February 21 due to a dispute over constructing a border outpost. On March 3, Afghan and Pakistani border forces exchanged heavy fire at the crossing, resulting in the death of an Afghan soldier.

Even beyond the TTP insurgency, Pakistan now alleges Afghan involvement in broader security threats. Citing the deadly March 11 train hijacking by Baloch separatists, Islamabad claimed that the hijackers contacted handlers in Afghanistan for instructions. Meanwhile, Pakistan has accelerated the deportation of Afghan refugees, adding another layer of diplomatic strain. Security conditions remain precarious as TTP attacks and clashes with Pakistani forces persist without any sign of de-escalation.

At the same time, the Taliban has strengthened ties with India, Pakistan’s regional rival. On Jan. 8, 2025, India's foreign secretary met with Afghanistan's acting foreign minister in Dubai, marking their highest-level diplomatic engagement since the Taliban takeover. During the meeting, Afghanistan explored utilizing Iran’s Chabahar Port for trade, clearly signaling its intent to reduce dependence on Pakistani trade routes. As a landlocked nation, Afghanistan has long depended on Pakistani seaports.

This underscores Afghanistan’s intent to minimize its strategic reliance on Pakistan, aiming for greater policy freedom. Thus, Afghanistan may adopt a more assertive stance against Pakistan in the coming days.

Pakistan-Afghanistan relations remain fragile, shaped by historical disputes, security threats, and shifting alliances. Pakistan continues to accuse the Taliban of backing the TTP, while the Taliban’s defiance hinders any resolution. Meanwhile, Kabul’s growing ties with India further complicate the conflict. Without meaningful dialogue and cooperation, long-term stability remains uncertain.