Zafarullah Jamali, the Pakistan Prime Minister, disclosed the appointment of Khan in an interview with state-run Indian Doordarshan television.
The nomination of Khan for the key assignment in India comes as the two countries move closer to resuming long-stalled dialogue.
On Tuesday, New Delhi appointed Shiv Shankar Menon, who was ambassador in Beijing, to head the Indian mission in Islamabad as High Commissioner.
Khan was Pakistan's ambassador in Beijing until Saturday’s appointment. He has experience at the United Nations and has held top diplomatic assignments in Belgium and the Central Asian republic of Kazakhstan.
He participated in the negotiations at Geneva in 1988 that culminated in an international accord for the withdrawal of forces of the former Soviet Union from Afghanistan.
Known as an expert on Afghan affairs, he has authored a book on the war-torn country. Khan functioned as spokesman at the foreign ministry in Islamabad after the September 11 attack.
"Pakistan has appointed a senior and experienced diplomat and the choice shows the earnestness with which Islamabad regards the resumption of dialogue with India," former foreign secretary Tanvir Ahmed said.
Pakistan's decision clears the way for restoration of ambassador-level diplomatic relations between the countries after a gap of nearly 18 months.
|Vajpayee: the first step|
It described the appointments of the high commissioners as a "step forward" in the ongoing diplomatic contact to put back on track the bilateral dialogue process.
The two countries have fought three wars since their independence in 1947, two of them over the Himalayan state of Kashmir which is split between them and is claimed by both.
Atal Behari Vajpayee, the Indian Prime Minister, on 18 April offered a hand of friendship to Pakistan which had been consistently calling for resumption of bilateral talks on Kashmir and all outstanding issues.
Days later, Jamali made an ice-breaking phone call to Vajpayee inviting him to Pakistan for talks and offering to travel to India.