"Obviously, the issue of counter-terrorism was both the first issue and the last issue on their agenda," State Department spokesperson Victoria Nuland said.
Both Clinton and Khar are in New York to attend the annual session of the United Nations General Assembly.
Khar has come in place of Prime Minister Yousuf Raza Gilani, who cancelled his trip to the US at the last minute in view of the deteriorating flood situation in Sindh.
"The Secretary and Foreign Minister Khar of Pakistan met for three and a half hours this afternoon. They reviewed the full range of bilateral and regional issues on our shared agenda," Nuland said in a late night statement yesterday.
However, there was no explanation as to why the meeting, which was initially scheduled for 30 minutes, dragged on for three and half hours.
It is understood that the Secretary of State pressed her Pakistani counterpart on the need for Pakistan to take strong and effective action against the Haqqani network, which US officials allege was involved in the recent terrorist attack on the US Embassy in Kabul.
"The meeting was very substantial, very candid," Nuland said.
"The Secretary and the minister have a very strong relationship and they are both committed to working intensively together and with their governments to take our bilateral relationship forward," she said.