The government released few details about Imran Khan's meeting with Khalilzad, saying he "reiterated Pakistan's commitment to facilitate the peace process in Afghanistan."
In a statement, it said Khalilzad briefed Khan "on his recent visits to the region to muster support for the Afghan reconciliation process."
Earlier, on second day of his visit to Islamabad, Khalilzad also met with Pakistan's Foreign Minister Shah Mahmood Qureshi to thank him for his continued support in advancing the peace process.
According to the foreign ministry's statement, Qureshi assured Khalilzad of Pakistan's support for a peace process, which has suffered a setback because of the Taliban's persistent refusal to directly talk to the Afghan government in Kabul.
Washington hopes Pakistan can help end the conflict by convincing the Taliban to meet with the U.S. and Afghan officials.
Islamabad says its influence on the Taliban is overstated but it will do whatever is possible for peace amid speculations that efforts were underway to arrange another meeting between Khalilzad and the Taliban in Pakistan.
But, Taliban spokesman Zabiullah Mujahid in a tweet said there was no reality to the suggestion about a Taliban meeting with Khalilzad in Islamabad.
On his previous visits to the region, Khalilzad held talks with the Taliban in their Mideast headquarters in Qatar.
It was in 2015 when Pakistan hosted the first ever face-to-face talks between Kabul and the Afghan Taliban, but the second round of the scheduled talks collapsed when Afghan government announced the death of Taliban founder Mullah Mohammed Omar.
It strained ties between Kabul and Islamabad at the time.
On Thursday, Afghan President Ashraf Ghani called Khan to discuss how to advance the peace process.
Pakistan's government says Khan assured Ghani that his country was making sincere efforts for a negotiated settlement of the conflict in Afghanistan through an inclusive peace process, as part of a shared responsibility.
Islamabad says only an intra-Afghan dialogue will lead to peace and stability in Afghanistan.
Associated Press Writer Amir Shah in Kabul, Afghanistan, contributed to this report.