The meeting was held in the Prime Minister House in Islamabad.
Official sources said that security matters were discussed in the meeting which was more of a courtesy call.
Local media reported that the prime minister discussed policy guidelines and internal security with the spy chief.
Sharif also appreciated the role the ISI has played in the anti-terrorism war.
Mukhtar was appointed as ISI's director general about two weeks ago after Lt Gen Rizwan Akhtar was appointed as president of army-run National Defence University.
He has also experience of handling spy affairs as he also served in ISI as head of its counter-terrorism wing.
He has also direct experience of fighting militancy as he commanded a brigade in South Waziristan tribal district as a brigadier.
Mukhtar was commissioned in the Armoured Corps regiment in 1983. He is a graduate of the Command and Staff College Quetta, National Defense University Islamabad and War Course USA.
He had commanded a Mechanised Division, according to army.
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