The Foreign Ministry of Pakistan said that the prime minister will have meetings with the Iranian leadership, including Iran's Supreme Leader Ayatollah Ali Khamenei and President Hassan Rouhani.
"Besides issues relating to peace and security in the Gulf, bilateral matters and important regional developments will be discussed," a foreign ministry statement said.
This is the Pakistani prime minister's second visit to Iran this year.
Khan held a bilateral meeting with Rouhani on the sidelines of the 74th session of the United Nations General Assembly in New York in September.
Foreign Ministry spokesman Mohammad Faisal said on Thursday the prime minister will also visit Saudi Arabia after his visit to Iran.
Pakistani media has reported that Khan's visit to Iran and later to Saudi Arabia is aimed at mediating between the two countries.
Tensions have been rising between Iran and Saudi Arabia since Sept. 14 when two major Saudi oil facilities were attacked, forcing Saudi Arabia to cut half of its oil exports.
The Iran-allied Houthi rebels in Yemen claimed responsibility for the attacks, but the United States and Saudi Arabia have blamed Iran for being behind the attacks. Iran has repeatedly denied the charges.
A Pakistani Foreign Ministry official said Khan is "eager to do whatever he can to de-escalate tensions" between Iran and Saudi Arabia.
The official told Xinhua that the prime minister is not paying the visit to Iran on request by any country but it is "purely his personal initiative."
Meanwhile Iran's Foreign Minister Mohammad Javad Zarif on Saturday welcomed efforts by intermediaries to mediate between Tehran and Riyadh, Iranian Tasnim news agency reported.
"We don't have any choice but to talk to each other, and we have been open to talking to Saudi Arabia either directly or through intermediaries," Zarif was quoted as saying when asked about Pakistani prime minister's visit to Iran.