Khan was detained by a police team at the airport when he was on his way to board a flight to New Delhi, a police official said.
The separatist leader was taken to Police Station Saddar from where he is likely shifted to his residence and placed under house arrest, he said.
Khan was on his way to New Delhi apparently to take part in Pakistan Day celebrations at Pakistan High Commission tomorrow.
Other separatist leaders, who have participated in the Pakistan Day celebrations in the past, are currently under detention inside their homes or in jail.