The case was registered at Raman Police Station after Islamabad High Court (IHC) ordered the government to take legal action against "blasphemous Facebook pages".
"Sentiments of Muslims have been hurt by the content being shared on these pages," according to the FIR.
The relevant sections of blasphemy laws have been invoked against the alleged perpetrators of the crime, an official said.
Justice Shaukat Aziz Siddiqui of IHC on March 7 had ordered Interior Minister Nisar Ali Khan to take immediate action to eliminate access to blasphemous content on social media.
The IHC judge also ordered placement of alleged Facebook pages owners' names on the Exit Control List (ECL) so that they cannot escape the legal proceedings of the case.