The FIR was filed against "unknown persons" though India had named JeM chief Masood Azhar as mastermind of the strike. The Pathankot attack had led to the postponement of Indo-Pak Foreign Secretary-level talks.
It is a "step forward" in investigation and to bring the perpetrators of the attack to book, official sources said.
The FIR was registered at Counter-Terrorism Department (CTD) centre in Gujranwala, Punjab province, yesterday, after weeks of investigation into the case.
India has identified Azhar as the mastermind of the attack. It has also blamed his brother Rauf and five others for carrying out the attack.
The FIR has been lodged on the basis of information provided by National Security Adviser Ajit Doval that four attackers probably crossed from Pakistan into India and attacked the airbase on January 2.
The FIR number 06/2016 was lodged under sections 302, 324 and 109 of the Pakistan Penal Code, and sections 7 and 21-I of the Anti-Terrorism Act.
Pakistan Prime Minister Nawaz Sharif had formed the six- member investigation team headed by Additional Inspector General of Punjab's CTD Rai Tahir to probe India's assertion that JeM was behind the attack.
