The US still considers Pakistan a key ally in its "war on terror", President George W Bush has told visiting Pakistani PM Yousuf Raza Gilani, reported BBC.
After talks, Mr Bush said Mr Gilani had made a strong commitment to securing Pakistan's border with Afghanistan.
The issue has caused strain in recent months, with the US urging Pakistan to move against Islamic militants.
The talks came as a top al-Qaeda figure was reported to have been killed in a missile strike in the border area.
Midhat Mursi al-Sayid Umar, a leading chemical weapons expert who the US says trained militants in Afghanistan, was reportedly killed along with six others in South Waziristan in a strike on Monday.
It was suspected to be a strike by US forces, but this has not been confirmed.
Mr Gilani called on the US not to act "unilaterally" against Islamic militants in Pakistan, but added that "basically Americans are a little impatient".
"We must have more co-operation with each other and it's our job because we are fighting the war for ourselves," he said.
US and Afghan officials say Taleban and al-Qaeda militants have established their strongholds on Pakistan's western border from where they carry out attacks into Afghanistan.
The US has recently expressed misgivings about Pakistan's handling of Islamic militancy in the area, while Pakistan has complained that attacks inside its borders could threaten bilateral relations.
In a joint news conference following the talks, Mr Bush twice said that he respected Pakistan's sovereignty.
He said the pair had talked of the "common threat" posed by extremists, and he praised the Pakistani prime minister as a reliable partner in tackling terrorism.
"Pakistan is a strong ally," Mr Bush told reporters.
On his first trip to Washington since taking power in February, Mr Gilani sought to assure the US that most Pakistanis want peace and want to co-operate.
"We are committed to fight against those extremists and terrorists who are destroying and making the world not safe.
"This is our own war - this is a war which is against Pakistan," he said.
But the BBC's Kim Ghattas in Washington says that despite Mr Bush's public praise, it was expected that Mr Gilani would hear some tough words.
Washington has said it is concerned about peace deals that Islamabad has been signing with some of the radical groups in its western tribal-dominated areas.
The Pakistani government says the peace deals will bring stability to the volatile regions.
But Washington argues that this gives the militants too much room to manoeuvre and increases the threat to Nato troops across the border.
US military commanders have warned that if there is ever another attack against the US, it will be planned in those areas.
But, our correspondent says, there will be statements of support - and possibly action - to back them as the US seems keen to encourage the fragile transition from military to civilian rule in Islamabad.
In recent months the US and its allies have pledged hundreds of millions of dollars in military and other forms of assistance to help Pakistan's new government tackle militancy in border areas.
Earlier this month, defense secretary Robert Gates said he was considering sending additional troops to Afghanistan to counter the flow of insurgents from Pakistan.