Khan's office said his visit was part of an initiative "to promote peace and security in the region", and that he will hold talks with Iran's supreme leader Ayatollah Ali Khamenei and President Hassan Rouhani.
It will be his second visit this year to Iran, which shares a border of around 1,000 kilometres (620 miles) with Pakistan.
In a press briefing last week, a spokesman for Pakistan's foreign office said Khan was expected to visit Saudi Arabia, without providing further details.
Khan said last month that both the United States and Saudi Arabia had asked him to mediate with Iran to defuse tensions in the Gulf.
There have been a spate of still unexplained attacks on shipping in and around the vital seaway involving Iran and Western powers, as well as drone attacks on Saudi oil installations.
Washington accused Tehran of attacking the vessels with mines and to be behind the drone assault, something Tehran strongly denies.
Pakistan has strong relations with Saudi Arabia - over 2.5 million of its nationals live and work in the kingdom - but also maintains good relations with Iran and represents Tehran's consular interests in the United States.
Khan met both US President Donald Trump and Iranian President Hassan Rouhani at the United Nations last month, shortly after he visited Crown Prince Mohammed bin Salman in Saudi Arabia.
Follow us on Twitter: @The_NewArab
