Mrs Clinton said any peace deal in Afghanistan would not succeed unless Pakistan was part of the process.
She expressed Washington's "strong commitment" to relations with Pakistan.
She was speaking after meeting Pakistani leaders on a seven-hour previously unannounced trip aimed at repairing ties badly damaged by the 2 May US raid that killed al-Qaeda chief Osama Bin Laden.
MomentumMrs Clinton said that the US had "absolutely no evidence that anyone at the highest level of the Pakistani government" knew where Bin Laden was and said she would return to Washington "ever more committed" to the relationship.
"This was an especially important visit because we have reached a turning point. Osama Bin Laden is dead but al-Qaeda and his syndicate of terror remain a serious threat to us both," she said.
"There is a momentum toward political reconciliation in Afghanistan but the insurgency continues to operate from safe havens here in Pakistan," she added, saying she believed that Pakistan and the US had the same goals.
It is the first such high-level visit to Pakistan since the killing of Bin Laden on 2 May. The American special forces raid on Bin Laden's hideout in Abbottabad prompted protests from Islamabad.
Mrs Clinton was accompanied on her visit by the chairman of the US Joint Chiefs of Staff, Adm Mike Mullen.
The pair held meetings with senior Pakistani politicians and army officers to plead for greater co-operation in the war against the Taliban and al-Qaeda.
She called on Islamabad to take "decisive steps" in the days ahead to fight terrorism.
Mrs Clinton denied that the meetings, held under tight security, were tense and said she had heard Pakistan commit to "some very specific action" against militants for which the country "deserved more credit".
Her visit comes a day after the US announced it was withdrawing some of its troops from Pakistan, at Islamabad's request.
In what correspondents say was perhaps an attempt to smooth ruffled Pakistani feathers over the killing, Mrs Clinton acknowledged the ''sacrifices made every single day by the men and women Pakistan's military and its citizens".
The ground was prepared by Senator John Kerry and the Special Representative for Afghanistan and Pakistan, Marc Grossman. The decision to visit was taken on Wednesday but kept under wraps for security reasons.
The BBC's Kim Ghattas - who is travelling with Mrs Clinton - says that she arrived in Pakistan surrounded by intense security, her 20-car armoured motorcade racing through the city to the presidential palace with helicopters flying overhead.
Stone-faced
Relations between US and Pakistan are always complex and fragile but they are particularly volatile at the moment.
Our correspondent says that Mrs Clinton has met all of Pakistan's top officials several times before and is usually adept at smiley conversation for the cameras.
But this time she sat fairly stone-faced at the start of her meeting with Pakistan's president, prime minister, foreign secretary and army chief.
Some in Washington believe that Pakistani intelligence works closely with violent extremist groups. Suspicion is rife that some in Pakistan knew of Osama Bin Laden's hiding place all along.
Meanwhile, US media reports say that Pakistan will allow the CIA to examine Bin Laden's compound in Abbottabad.