Shouting anti-India and pro-Pakistan slogans, the protesters were seen surrounding the director as he arrived at the airport to leave for Lahore.
The protesters were seen in a video asking the director why he did not make movies on the Indian intelligence agency Research and Analysis Wing (RAW) activities in Pakistan.
One of the protesters was also seen raising a show in his hand.
"You people send Jhadav and kill hundreds here, why don't you make a movie about it," a protester was quoted as saying to Dawn News.
Khan had directed films like 'Phantom' and 'Bajrangi Bhaijaan'.
Phantom's screenplay was written in coordination with author Hussain Zaidi's book Mumbai Avengers on the aftermath of 26/11 Mumbai attacks.
Meanwhile, the director urged the media to not give attention to the protesters.
"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 tweeted.
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