Demonstrators shouting anti-India slogans mobbed the Bollywood director, loudly asking him why he did not make movies depicting the role played by the Indian intelligence agency RAW in Pakistan.
At least one man waved a shoe at Khan who did not respond to the ruckus at the departure lounge, Dawn reported.
"You people send Jhadav and kill hundreds here. Why don't you make a movie about it?" a protester asked the 'Phantom' director, referring to alleged RAW official Kulbhushan Jhadav who has been arrested in Pakistan.
Starring Saif Ali Khan and Katrina Kaif, 'Phantom' is about a retired Indian Army officer who leads a mission to kill Pakistani terrorist leader Hafiz Saeed.
Another shoe-wielding man chased Khan to the departure lounge, warning the director about "Indian conspiracies against the Pakistan Army", Dawn said.
Kabir Khan tweeted about the incident soon after. Here's what he had to say:
"To media on both sides: 12 screaming lunatics with a mobile phone camera is not news. Please don't give them the attention they want. Ignore."
Khan's 'Bajrangi Bhaijaan' received a warm response in Pakistan, where Indian movies are always in great demand.
'Phantom', based on a novel by S. Hussain Zaidi, was banned by the Lahore High Court.
Khan arrived here to take part in a conference and said he was a firm believer in India's secular fabric and in the friendship between India and Pakistan.