The pilotless aircraft Burraq destroyed the rebel hideout in Shawal area of North Waziristan near the Afghanistan border.
"The first-ever use of Pakistan-made Burraq drone today hit a terrorist compound in Shawal Valley killing three high profile terrorists," Military spokesman Major General Asim Bajwa tweeted.
The remotely-piloted aircraft 'Burraq' and laser-guided missile 'Burq' were tested on March 14, taking Pakistan a step closer to acquiring the technology it has long demanded from the US.
The Pakistan military has been battling militants in Shawal as part of an offensive launched in June 2014 in North Waziristan, a longtime stronghold of al-Qaida and other armed groups along the Afghan border.
Pakistan started working on its drones after US drones, operated by CIA, sometimes killed civilians in tribal region, sparking anger in the country. Pakistan opposes US drone attacks and frequently lodges protests over it but America has refused to stop them.