Armitage, accompanied by Assistant Secretary of State for South Asian Affairs, Christina Rocca, met General Musharraf early on Monday at army headquarters in Rawalpindi next to Islamabad, a Pakistani official said.
No details of their discussions were released, though Armitage had earlier praised the Pakistani president’s campaign against “extremism”.
On a Sunday day-trip to the Afghan cities of Kandahar and Kabul, Armitage expressed his pleasure at two operations last week by Pakistan's military against suspected “terrorists”, including a deadly raid on an alleged Taliban and al-Qaida hideout near the border with Afghanistan.
After talks with Afghan leaders, the envoy said he noted "with great approval the tremendous effort in the last couple of days of the Pakistani forces against Taliban and al-Qaida which resulted in the deaths of some and the capture of others."
Blowing hot and cold
Armitage's comments were something of a U-turn after telling US lawmakers last week he did not believe that all levels of Pakistan's military were committed to the US-led hunt for Taliban and al-Qaida fighters.
Last Thursday Pakistani forces demonstrated their allegiance - in front of reporters flown in specially by the army - by besieging suspected Taliban and al-Qaida fighters believed to have taken part in attacks on US troops from Afghanistan's Shkin district.
They captured 18 and killed eight fighters in the day-long air and ground battle, in which two Pakistani troops were also killed.
Before 11 September, 2001 Pakistan was one of only two official allies the Taliban had, the other being Saudi Arabia.
The raid was launched on Thursday, the same day Armitage was originally due to arrive in Islamabad before his trip was delayed by two days.
On Saturday Pakistani troops raided and dismantled an empty guerrilla training camp in northern Pakistan's Diamer district, but the military said the "terrorists" who had trained there were not al-Qaida members and suggested they were a group of Pakistani sectarian fighters.
'Our enemies too'
Armitage said he would discuss with Musharraf the overall state of the hunt for fighters believed to be launching attacks inside Afghanistan from Pakistan's tribal border areas.
"I obviously want to talk with him about his recent activities against al-Qaida and Taliban; after all these are our enemies too, they're not just enemies of Afghanistan or enemies of president Musharraf," he told reporters in Kabul.
US President George Bush and General Pervez Musharraf press the flesh
Until Pakistan was co-opted into the US-led “war on terror” ,following the 11 September 2001 attacks, the Taliban was not an enemy.
In fact Pakistan was one of only two official allies the Taliban had, the other being Saudi Arabia.
Armitage and Rocca will later hold talks with defence ministry officials and meet Foreign Minister Khurshid Mahmud Kasuri for a working lunch, the official said.
'No extremists' pledge
Their visit comes amid rising US and Afghan government frustration at attacks by resurgent Taliban from Pakistan's tribal border areas.
There are also fears that six-month-old peace initiatives with India are floundering in the wake of Pakistan’s recent missile tests and ongoing violence between the Indian army and Islamic fighters in disputed Kashmir.
In Afghanistan, the Taliban attacks are driving aid workers away from the south and east of Afghanistan, leaving desperately needed development projects suspended.
In Kabul Armitage also praised Musharraf for speaking out against "extremists". Musharraf told a business dinner on Friday that extremism was the greatest threat facing Pakistan and vowed to keep fighting it.
"There will be no extremists here in Pakistan," he said in comments carried by state media.