Who Really Runs Pakistan?

 Early Post-Independence Suspicions (1947–1951)

From the very outset of Pakistan’s history, there were signs that real power might lie outside the civilian leadership. In October 1947, as fighting started in Kashmir, Jinnah (then Governor-General) ordered the army to move into Kashmir – only to have his British commander-in-chief refuse to comply. The British high command’s “stand down” order effectively overruled Jinnah’s wishes, foreshadowing a pattern of military assertiveness over civilian decisions. A year later, in September 1948, Jinnah’s own death became shrouded in controversy. Critically ill, he was flown from Quetta to Karachi with little official fanfare – greeted only by a military secretary, an ambulance and a car. Disturbingly, the ambulance broke down just four miles into the journey, forcing a nearly one-hour delay before a replacement arrived. Jinnah spent his final hours stranded on a roadside, which many later found “inexplicable” and suspicious, fueling speculation that elements of the establishment failed the ailing leader.

The uncertainty only deepened in 1951 with the assassination of Pakistan’s first Prime Minister, Liaquat Ali Khan. He was shot dead at a public rally in Rawalpindi. The assassin was immediately killed by police, cutting off any chance to interrogate him. Questions soon arose in Parliament about possible official complicity. Members of the National Assembly alleged that the family of Liaquat’s assassin was mysteriously receiving a generous government pension. One legislator even noted that the police officer who shot the assassin went on to acquire enough wealth to start a business (a textile mill) shortly afterward. Such revelations gave rise to credible allegations that powerful figures may have orchestrated a cover-up in Liaquat’s murder. Though no inquiry ever proved these suspicions, the episode ingrained a public perception that shadowy forces within the state – possibly within the military or intelligence establishment – were pulling strings behind the scenes.

The Military Takes Control (1958–1971)

By the late 1950s, the Pakistani military had decisively entered the political arena. In October 1958, the country’s first coup d’état unfolded: President Iskander Mirza abrogated the constitution and declared martial law with General Ayub Khan as Chief Martial Law Administrator – only to be promptly deposed by Ayub Khan himself weeks later, as the general sent the president into exile and assumed power directly. This pattern – generals toppling the very civilians who appointed them – would recur throughout Pakistan’s history. General Ayub Khan’s martial law regime (1958–1969) marked the formal beginning of direct military rule. Even when Ayub stepped down in 1969 amid public unrest, he handed over power not to any elected representative but to another general, Yahya Khan. Yahya in turn clung to authority until the catastrophe of 1971 forced his resignation.

During Ayub Khan’s rule, a key flashpoint was the 1965 presidential election, when Fatima Jinnah (sister of Muhammad Ali Jinnah) challenged Ayub’s dictatorial presidency. Fatima Jinnah, revered as Madar-e-Millat (“Mother of the Nation”), galvanized huge crowds and threatened Ayub’s grip on power. The regime reacted with a campaign of harassment and character assassination against her. Ayub’s propagandists painted Fatima Jinnah as a traitor; one official pamphlet ludicrously accused her of plotting with Pashtun nationalist Khan Abdul Ghaffar Khan to break up Pakistan by creating a “Pashtunistan”. Behind the scenes, Ayub’s government heavily rigged the electoral process. The 80,000 “basic democrats” (local councilors) who formed the electoral college were largely handpicked or bribed to vote for Ayub. Despite these underhanded tactics, contemporary accounts suggest Fatima Jinnah still won in major cities like Karachi and Dhaka – yet Ayub was declared the victor. Fatima Jinnah was not just denied victory; she was humiliated by the military establishment’s smear campaign. Tragically, she died two years later in 1967 under mysterious circumstances. The official cause was heart failure, but no autopsy was conducted. Rumors spread of foul play, and indeed many believe she was actually murdered in her Karachi home. Decades later, a court petition and media reports would call her death “an unsolved criminal case,” alleging that Fatima Jinnah was eliminated by those threatened by her outspokenness against military rule.

The ultimate proof of the military’s supremacy over the civilian leadership in this era came with the 1971 secession of East Pakistan, leading to the creation of Bangladesh. In Pakistan’s first real nationwide democratic election (1970), Sheikh Mujibur Rahman’s Awami League won a clear majority, sweeping almost all seats in East Pakistan. The proper democratic course was to invite Mujib to form the government. Instead, the West Pakistani military regime (General Yahya Khan and allies like Zulfikar Ali Bhutto) refused to honor the election results, blocking Mujib from becoming prime minister. As protests and civil disobedience gripped East Pakistan, Yahya Khan chose a military solution: on March 25, 1971 his army launched “Operation Searchlight,” a brutal crackdown in Dhaka and other cities. This ignited a civil war. The army’s campaign escalated into atrocities – mass killings and repression of the Bengali population – which only strengthened the resentment which soon transformed into independence movement. By December 1971, after a brief India-Pakistan war in which the Pakistani military conceded, East Pakistan broke away as the new nation of Bangladesh. The loss of half the country was a direct outcome of the junta’s obstinacy and militaristic mindset. A later inquiry, the Hamoodur Rahman Commission, harshly criticized the generals’ actions. But the damage was done: Pakistan’s army had demonstrated it would unleash war on its own citizens rather than to cede power to elected civilians.

Political Engineering and Coups (1977–1990s)

After the trauma of 1971, Pakistan did experience a brief democratic interlude under Zulfikar Ali Bhutto, who was himself part of the junta causing cessation of East Pakistan.  The military’s influence never truly waned. In July 1977, Army Chief General Zia-ul-Haq toppled Bhutto’s elected government in a coup. Zia imposed the country’s third martial law, jailed Prime Minister Bhutto, and later sent him to the gallows under a contentious court verdict. General Zia then ruled with an iron fist for 11 years, entrenching the army’s role further. He even amended the constitution (via the infamous Eighth Amendment) to cement extraordinary powers for himself as President – including the authority to dismiss elected governments. This legal change outlasted Zia’s own lifetime and was repeatedly used in the late 1980s and 1990s to sack governments that fell afoul of the establishment.

Under Zia and subsequent military-backed presidents, Pakistan’s politics became a managed democracy at best. Elections were held in the post-Zia period, but the playing field was blatantly skewed by the army and intelligence agencies. One glaring example was the 1990 general election. Fearful of Benazir Bhutto’s Pakistan Peoples Party (PPP) returning to power, the military high command orchestrated the formation of a conservative alliance, the Islami Jamhoori Ittehad (IJI), to oppose her. Decades later, the details of this operation came to light in the Asghar Khan Case: a petition by a former Air Force chief that eventually led to a Supreme Court judgment. Testimony in that case confirmed that the ISI (Inter-Services Intelligence) doled out large sums of money to select politicians in 1990 to buy their loyalty and manipulate the election outcome. A former ISI chief, Gen. Asad Durrani, gave a sworn affidavit admitting that he oversaw distribution of a secret “slush fund” to political figures to ensure Bhutto’s defeat. The Supreme Court in 2012 deemed this an unconstitutional subversion of the democratic process – yet tellingly, no military officials were ever punished for it. The Asghar Khan case stands as formal acknowledgement that Pakistan’s military elite has meddled in elections, covertly shaping governments to its liking.

In October 1999, the military struck openly yet again. General Pervez Musharraf led a coup against Prime Minister Nawaz Sharif’s government after a dispute over control of the army. Musharraf suspended the constitution and assumed power, becoming Pakistan’s fourth military ruler. This coup, like those before, was justified by lofty promises of ending corruption and restoring stability; in reality it reaffirmed that the army reserved for itself the ultimate veto over Pakistani politics. Musharraf’s dictatorship lasted nearly a decade, during which time he too tried to tailor the political landscape by sidelining the mainstream parties and promoting a new King’s party. While Pakistan returned to formal democracy in 2008 after Musharraf’s exit, the precedent of periodic coups and constant behind-the-scenes manipulation had been well established.

The “Hybrid” Era and the Rise of Imran Khan (2008–2022)

From 2008 onward, Pakistan’s military ostensibly stepped back from direct rule. However, analysts often described the system as a “hybrid regime,” where the civilian government was continually influenced by the army in key domains – from foreign policy and national security to strategic economic decisions. The military and ISI maintained an outsized role, and no Prime Minister still managed to serve a full five-year term.. Typically, civilian leaders who tried to assert authority – especially over military affairs – found themselves weakened by scandals, street agitations, or court cases, in patterns many believe were abetted by the establishment. For instance, three-time PM Nawaz Sharif was ousted in 2017 on charges stemming from the Panama Papers leak. While the judiciary formally executed that removal, it came after Sharif had clashed with the army on policy matters, and observers noted that the process bore the hallmarks of a “soft coup” using judicial and bureaucratic levers. Indeed, history shows that whenever a civilian leader “gets too big for their boots,” the military finds a way to cut them down.

It was in this setting that cricketer-turned-politician Imran Khan rose to prominence. By the 2010s, Khan positioned himself as a reformer against the traditional political elite. He also aligned closely with the military’s worldview on various issues. In the 2018 elections, many rivals alleged that the military establishment tilted the field in Imran Khan’s favor. There were reports of serious irregularities on election day such as the failing of Election Commission’s Results Transmission System (RTS). A strong counter narrative is that irregularities were engineered to prevent Khan’s party from achieving majority on its own. This matches with the military’s desire to keep control of the Civilian governments. There were reports of influencing independent winning candidates to join Khan. Nevertheless, Khan’s party, the Pakistan Tehreek-e-Insaf (PTI), emerged victorious and he became prime minister. Regardless of those 2018 controversies, it is widely accepted that Khan’s government initially enjoyed the tacit (some say explicit) backing of the generals. This civil-military cooperation, however, was not to last.

By late 2021 and early 2022, rifts emerged between Imran Khan and the army leadership (then led by General Qamar Javed Bajwa). Disagreements over key appointments – notably the ISI director-general post – and Khan’s independent streak in foreign policy (for example, his continued closeness with Pakistan’s erstwhile allies in Afghanistan, or his overtures to Russia/China against U.S. advice) reportedly soured the relationship. It is widely accepted that the opposition started movement against Khan’s government with the backing of the generals and moved a no-confidence motion in Parliament in March 2022. Tellingly, the military declared it was “neutral” during this political crisis meaning they no longer support Khan’s government. The no-confidence vote succeeded in April 2022, ending Imran Khan’s tenure. This was made possible only because of military’s support for the opposition made many allies in the coalition government and few members of PTI vote against the government. Khan bluntly accused “foreign conspirators” and local “Mir Jafar” traitors (alluding to the military) of orchestrating his ouster. While the army denied any role, it was apparent that Khan’s downfall followed the familiar script: once the “all-powerful military establishment” withdrew support, his government quickly unraveled. In Pakistan’s power politics, losing the establishment’s favor often proves fatal for elected leaders. Khan’s foreign conspiracy theory also holds ground because of his tilt towards Russia and China as opposed to U.S. which has always been closer to the generals.

2023: The Mask Comes Off – Crackdown on Imran Khan and PTI

If earlier decades provided subtle or plausible deniability about who really pulls the strings in Pakistan, the events of 2023 removed any remaining doubt. In the aftermath of Imran Khan’s ouster, as he agitated for early elections and rallied huge crowds, the military establishment moved decisively to crush him and his party. This campaign intensified dramatically after May 9, 2023 – the day Khan was briefly arrested on corruption charges, sparking spontaneous protests by PTI supporters nationwide. Some of those protests turned violent, with angry mobs even attacking symbols of the army’s influence (such as corps commanders’ residences and memorials). The reaction from the state was swift and severe: the PTI was to be dismantled at all costs.

Over the following weeks and months, Pakistan witnessed an unprecedented crackdown on a political party. Thousands of PTI workers and virtually the entire senior leadership were arrested or went into hiding. Notably, many top figures who had been staunch Imran Khan loyalists for years suddenly defected. Press conference after press conference featured PTI stalwarts—often appearing strained or shaken—announcing they were quitting the party and condemning the May 9 violence. The pattern and scale of these reversals were so extraordinary that it raised immediate questions. Khan himself stated that his people were “under pressure” to leave, hinting at coercion by “unknown” forces. It was however quite obvious who those forces were. As the Guardian reported, there was “little question among analysts who is orchestrating the arrests and resignations” – it was being directed by the army’s top command. In effect, the new Army Chief, General Asim Munir, and his intelligence agencies systematically set about breaking PTI’s structure, aiming to eliminate Imran Khan’s political future.

Evidence of heavy-handed involvement by the military and intelligence agencies in this crackdown is plentiful. Many PTI leaders were detained under vague anti-terrorism charges, then handed over to the ISI for interrogation. Numerous accounts emerged of severe abuse. One senior party leader (speaking anonymously for safety) described how interrogators “tied my feet and hung me upside down,” using him as a punching bag to beat him into submission. They threatened to arrest his entire family unless he quit PTI – ultimately forcing him to publicly resign from the party to gain release and safety for his family. Such stories were echoed by others: activists and even family members of PTI associates were reportedly abducted or harassed, and told that all troubles would end if they simply disowned PTI. Human rights groups noted a resurgence of the military’s notorious “disappearance” tactics during this period. For example, a prominent pro-PTI TV anchor, Imran Riaz Khan, went missing after being picked up by security agents in May 2023 and remained unaccounted for several months. Similarly, the brother of Imran Khan’s former chief of staff was abducted from his home – plainly as leverage to intimidate the actual political target, who was abroad. Even individuals not formally in PTI but critical of the military, such as lawyer and activist Jibran Nasir, were snatched off the streets by unidentified men. The message was chillingly clear: no dissent would be tolerated.

Alongside the brute force, there was legal and political engineering to erase PTI’s presence. Under pressure from the establishment, courts and election authorities began entertaining moves to ban PTI outright and disqualify Imran Khan. In August 2023, Khan was convicted on a dubious corruption charge (the Toshakhana case) and imprisoned, effectively barring him from contesting elections. Dozens of other PTI lawmakers were also entangled in cases and disqualified. The remaining PTI members who refused to abandon the party found their businesses suddenly sealed and travel restricted – economic strangulation to complement the legal crackdown.

Perhaps the most striking sign of where real power lay was the revival of military courts to try civilians. Following the May 9 incidents, the government (seen as acting on the army’s behest) sanctioned the trial of rioters under the Army Act – meaning military officers as judges, and summary proceedings with no transparent due process. This decision blatantly undermined the civilian justice system. By October 2023, a Supreme Court bench initially did strike down these military trials of civilians as unconstitutional. But this relief was short-lived; a few months later, a reconstituted Supreme Court inexplicably reversed course and allowed military trials to proceed. The reconstitution of Supreme Court was effected by an amendment in the Constitution which was passed with the help of army pressurizing the political figures in voting in its favor. In May 2025, the manipulated Pakistan’s apex court even upheld legal changes that empowered the army to prosecute civilians for protest-related offenses. Such outcomes strongly indicated that the judiciary itself was under intense influence or even under outright control of the establishment. As a Dawn analysis grimly observed, “Civilian judges have revived a law first introduced by a military dictator, Ayub Khan, allowing the court martial of civilians”. In other words, the courts conceded to the army’s demands, legitimizing a parallel justice system run by the military – a step that effectively blurs any distinction between the rule of law and the rule of the generals.

Meanwhile, Pakistan’s democratic process lay in tatters. The national election due in late 2023 was postponed under various pretexts, conveniently giving the caretakers (seen as aligned with the establishment) more time to weaken the opposition. When the general election was finally held on February 8, 2024 (after a delay of several months), it was anything but free and fair. Leading up to it, there was a comprehensive pre-poll crackdown on Imran Khan’s PTI: thousands of PTI members and virtually all its top leadership were behind bars or forced out, and even the party’s name and election symbol were knocked off the ballot owing to a decision of the Supreme Court. On polling day, nationwide internet and cellular blackouts occurred, and reports suggested rigging and intimidation at polling stations, especially to benefit the parties favored by the establishment. Unsurprisingly, the result was a foregone conclusion – a victory for the faction of politicians deemed acceptable by the military, and a wipe-out for PTI. International observers and analysts widely labeled this election as “flawed” and reflective of the army’s heavy hand in politics. Pakistan’s democracy was reduced to a showpiece. The military was really choosing the candidates and the rulers, while civilians were just for display.

Conclusion: The Unseen Hand – Pakistan’s Real Rulers

Looking across 75+ years of Pakistan’s history, a consistent picture emerges. From the refusal to obey Jinnah’s orders in 1947, through the coups of 1958, 1977, and 1999, the meddling in elections like in 1965 and 1990, the suppression of political opponents, and the brazen manipulation of the system in 2023 – the through-line is the dominant role of the Pakistan Army in governance. The Army leadership, has repeatedly positioned itself as the ultimate arbiters of power, whether from the front (during outright martial law) or from behind the curtain in civilian guise. No major decision – be it war and peace, foreign alliances, or even the outcome of elections – escapes the army’s influence. Pakistan’s celebrated “democratic transitions” often prove in hindsight to be managed events, orchestrated or at least approved by the men in uniform.

Crucially, whenever a civilian leader or movement has challenged this arrangement, the institution of the army has closed ranks to reassert its primacy – as seen most recently with the crushing of Imran Khan’s popular movement. As one observer aptly noted, this is nothing anomalous but a continuation of a pattern that has “marred the country’s pathway to democracy since 1958”, with the military routinely asserting itself as “the most powerful political player in Pakistan”. In fact, a scholar bluntly described Pakistan’s power structure in 2023 by saying, “The military is the only party that is ruling the country.” History bears this out: all of Pakistan’s major parties – the Muslim League, PPP, and now PTI – have, at one time or another, been broken or co-opted by the security establishment. Civilian prime ministers have been removed through coups, court decisions, or intimidation whenever they crossed the implicit red lines set by the generals.

Thus, “Who really runs Pakistan?” The credible allegations and historical evidence all point to one answer: ultimate authority resides not with the elected representatives of the people, but with the leadership of the armed forces (and its intelligence arm). The Army, often in tandem with allied elites, has been the real ruler of Pakistan since independence – crafting the country’s destiny to suit its own institutional interests and in many cases personal interests of individuals. Even when not visible, it operates as the final decision-maker and power-broker, a state within the state. The wild events of 2022–2023 only pulled back the curtain, exposing the extent of the Army’s control over politics, the judiciary, and civil society. Pakistan’s so-called democracy has repeatedly been undermined by those wearing uniforms, and the nation’s history is filled with “credible allegations” that the military has subverted the civilian will time and again. In light of this record, it is hard to escape the conclusion that Pakistan’s real ruler is not any president or prime minister, but its Army – an institution that has come to see itself as the guardian of the state, accountable to none and decisively in charge.

References:

Stand Down Order (1947) - Wikipedia

https://en.wikipedia.org/wiki/Stand_Down_Order_(1947)

M.A. Jinnah: The tragic hero - Sp Supplements - DAWN.COM

https://www.dawn.com/news/1880968

Fresh inquiry into Liaquat’s murder urged - DAWN.COM

https://www.dawn.com/news/769460/fresh-inquiry-into-liaquats-murder-urged

How the Pakistan Army Overthrew Civilian Govts Over the Years

https://www.thequint.com/news/world/pakistan-prime-minister-president-government-military-takeovers-coups

Fatima’s election - Newspaper - DAWN.COM

https://www.dawn.com/news/1493578

How Fatima Jinnah died — an unsolved criminal case - DAWN.COM

https://www.dawn.com/news/1159181/how-fatima-jinnah-died-an-unsolved-criminal-case

Bangladesh Liberation War - Wikipedia

https://en.wikipedia.org/wiki/Bangladesh_Liberation_War

Imran Khan’s political games leave him isolated as Pakistan army destroys party | Imran Khan | The Guardian

https://www.theguardian.com/world/2023/jun/03/pakistan-imran-khan-pti-military-crackdown

Asghar Khan case - Newspaper - DAWN.COM

https://www.dawn.com/news/1463532

May 9 riots - Wikipedia

https://en.wikipedia.org/wiki/May_9_riots

Legalising Authoritarianism through Pakistan's Supreme Court

https://verfassungsblog.de/legalising-authoritarianism-through-pakistans-supreme-court/

Pakistan Supreme Court Hands Army More Power - LawBeat

https://lawbeat.in/top-stories/pakistan-supreme-court-hands-army-more-power-1400548

May 9 and military courts: What the SC decision means for civilians

https://www.dawn.com/news/1909718

Articles by Madiha Afzal’s Profile | The New York Times, The Washington Post, USA Today Journalist | Muck Rack

https://muckrack.com/madiha-afzal/articles