At least 20 members of the right-wing organisation, led by city unit chief Jwalit Mehta, targeted City Gold and Shiv theatres on Ashram Road this morning and smashed ticket windows and tore off posters of the film.
The film, directed by Rajkumar Hirani, is a satirical take on godmen and superstitions.
Policemen from Navrangpura station along with Deputy Commissioner of Police (Zone-1) Virendrasinh Yadav rushed to the spot, but the attackers had fled before that, police said.
However, Bajrang Dal owned up the attack and warned other theatres screening the film.
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"Around 15 to 20 of our members today went to these theatres, which are screening Aamir's film 'PK'. I am warning other theatres to stop the screening, otherwise we will intensify our protest in the city in the coming days," said Mehta.
He alleged that Aamir Khan had "hurt the religious sentiments" of Hindus by making fun of Hindu gods and devotees in the film.