For most of Pakistan’s eight-decade history, its courts were largely aligned with the country’s powerful military. They gave three coups a legal stamp of approval, disqualified dozens of politicians who had fallen out of favor with the generals, and turned a blind eye to the disappearances of political dissidents.

But with Pakistan in the grip of a political crisis that has sparked violent protests across the country, the judiciary has openly contradicted the military and emerged as a political force in its own right, analysts say. In recent months, as former Prime Minister Imran Khan has clashed with the military and current civilian government, the courts have issued ruling after ruling that have thwarted what many consider attempts by the military to sideline Mr. Khan from politics.

That defiance was highlighted earlier this month, when shortly after the authorities arrested Mr. Khan in a corruption inquiry, the courts declared his arrest unlawful, ordered his release and granted him bail.

It is a striking shift in Pakistan, where the military has long acted as the country’s ultimate political power broker: Directly ruling for over half of the country’s existence and acting as the veiled power behind civilian governments. And as the courts strike out on their own, they are injecting even more uncertainty into an already volatile political climate.

“So much of politics is about the military,” said Yasser Kureshi, a lecturer in South Asian studies at Oxford University. “Now that the court is a center of power in its own right, the court has worked out its ability to manipulate and mold politics in its interests.”

Analysts say the courts’ recent decisions — which effectively bolstered Mr. Khan’s political prospects — were as much a reflection of the judiciary’s budding political muscle as the military’s battered image.

Since Mr. Khan was ousted in a parliamentary no-confidence vote last year, he has railed vehemently at the generals and accused them of conspiring against him. His supporters have followed suit, disparaging military leaders on social media and recently storming military installations — once unimaginable scenes in a country where few have dared defy the security establishment.

Still, observers have cautioned against hailing the courts’ recent rulings as a shift to more independent or democratic politics in Pakistan. Many critics say that rather than acting as a more independent body looking to curb the military’s meddling, the courts are themselves enmeshed in politics, with some judges harboring deep loyalty to Mr. Khan.

“For the judiciary, there is this tinge of independence now that they are able to sustain some pressure from the establishment,” said Ali Qasmi, a lecturer at The Lahore University of Management Sciences. “At the same time there is a clear kind of pro-Imran Khan tendency within the courts as well.”

Senior judges in Pakistan play a substantial role in judicial appointments. The chief justice of the Supreme Court leads a commission that nominates judges for the top and high courts, who are then confirmed by a parliamentary committee. The mandatory retirement age is 65 for Supreme Court judges, and 62 for those in the high courts.

While the judiciary’s power does not come close to rivaling that of the military, in recent weeks military leaders have responded forcefully to tip the scales back in their favor and signal their ultimate dominance.

Last week, military officials announced that protesters who attacked military installations in response to Mr. Khan’s arrest would be tried in military — not civilian — courts. Several prominent leaders from Mr. Khan’s party have also been arrested by the police shortly after being granted bail. The moves, many observers say, were a military effort to intimidate Mr. Khan’s supporters and show that the courts alone cannot protect them.

For much of Pakistan’s turbulent history, the country’s judiciary was seen as a junior partner of the military, a tool used to legitimize its more direct forays into the political sphere. It offered legal justification when military generals seized power from civilian governments in 1958, then in 1977 and again in 1999. They also provided legal cover in the 1990s when the military dismissed two governments, both led by former Prime Minister Benazir Bhutto.

In the following decade, when a chief justice of the Supreme Court began to challenge the state’s use of power, the country’s military ruler, Gen. Pervez Musharraf, suspended the justice. The move caused uproar across the country and sparked a nationwide movement in support of the justice, who was eventually reinstated.

The interests of the courts and the military then seemed to coincide. Empowered by the notion of defending the public’s interests, the courts set out to root out the entrenched corruption among Pakistan’s political dynasties — just as those very dynasties were falling out with military leaders. In doing so, the courts also helped pave the way for Mr. Khan — the former cricket star who campaigned as an anti-corruption crusader and was embraced by the military — to win the election in 2018.

“Two things were happening in parallel: The first was the court was more empowered” after the nationwide movement to reinstate the ousted chief justice, said Saroop Ijaz, a senior counsel at Human Rights Watch, the international watchdog group. “And the second is the military realized an empowered court was a great partner to influence political outcomes, to send prime ministers home without a direct military intervention.”

But while military leaders appeared to withdraw their support for Mr. Khan early last year, many in the judiciary still viewed him as a partner in their anti-corruption purge, analysts say.

The growing rift between the military and courts surfaced in April, when the Supreme Court, led by Chief Justice Umar Ata Bandial, ruled that the current government’s attempt to delay local elections in two provinces, including the most populous, Punjab, was unconstitutional. At the time, the ruling was widely considered a boon for Mr. Khan’s political party, Pakistan Tehreek-e-Insaf or P.T.I.

A month later, the Supreme Court ordered Mr. Khan to be released from custody and soon afterward the Islamabad High Court granted him pre-emptive bail in several corruption cases he is facing.

Mr. Khan’s supporters say that his opponents are trying to have him arrested to prevent him from hitting the streets and whipping up support for his party ahead of the country’s general elections this fall.

Mr. Sharif’s government has already attempted to rein in the powers of Mr. Bandial, who has been accused of being politically aligned with Mr. Khan.

In March, Pakistan’s parliament passed a new law to curtail the powers of the chief justice, reassigning his unique powers — including the ability to convene a small panel of specific judges to hear cases — to a committee of three justices. But later that day, the Supreme Court issued an injunction, preventing the law from taking effect.

In doing so, the court showed that while its powers are limited and it has no ability to enforce its rulings, it is still a force to be reckoned with as the country barrels toward general elections this fall, analysts say.

That new dynamic, said Mr. Kureshi, the lecturer at Oxford University, “changes the game and changes the way in which political bargaining with these unelected institutions happens.”

Christina Goldbaum is a correspondent in the Kabul, Afghanistan, bureau. @cegoldbaum

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