His comments followed the deaths of at least 90 people in Afghanistan over the past two weeks in clashes blamed on Taliban fighters.
Afghan officials say Taliban rebels plot attacks from the safety of Pakistan's tribal frontier regions.
Musharraf's assurance came during a meeting on Saturday with a US Congressional delegation led by Arizona Republican John McCain.
"The president reiterated to the US delegation that Pakistan would not tolerate any terrorist activity across its borders," the foreign ministry said in a statement.
Pressure on Pakistan
Pakistan was the main supporter of the Taliban until it threw its weight behind the US in the wake of the attacks on the United States on 11 September, 2001.
US and Afghan officials have been urging Pakistan to do more to prevent cross-border movement of Taliban fighters, forced from power by a US-led offensive in late 2001.
But Pakistan says it has been doing all it can to prevent such activities, citing the arrest of hundreds of Taliban and members of al-Qaida.
The Pakistani statement said Musharraf called for the "timely exchange of intelligence" between Pakistan and Afghanistan to combat terrorism.
Afghan officials have also accused Pakistani troops of grabbing territory along their border and there have been some skirmishes between the country's forces in recent weeks. Pakistan denies the accusation.