The "Burraq" drone attacked a suspected militant hideout in the Shawal Valley, which has long been a militant stronghold on the border with Afghanistan, said Major General Asim Bajwa, the military's chief spokesman.
"Hit a terrorist compound in Shawal Valley killing (three) high profile terrorists," Bajwa said in a posting on his Twitter feed. He did not say when the drone strike happened or give any more details, according to Reuters.
Militants in the area identified one of the three people killed in the Sunday night strike as Nizam Wazir, a faction leader allied with the Pakistani Taliban. Wazir was being buried on Monday, they said.
Government forces launched an offensive against Pakistani Taliban militants in semi-autonomous ethnic Pashtun regions along the Afghan border last year.
The military expanded the offensive into the Shawal Valley last month, with the use of both ground troops and aircraft.
The government has for years denounced US drone strikes in Pakistan as a violation of sovereignty, with US drones having killed more than 2,400 people in Pakistan since 2004, according to the independent London-based Bureau of Investigative Journalism, which monitors strikes through news reports.
The US strikes have enraged many members of the public in Pakistan, fuelling anti-US sentiment and anger towards Pakistani governments seen as too accommodating of US demands in its war on militancy.
Pakistan first successfully tested the Burraq drone in March with the military hailing it as "a force multiplier in the anti-terror campaign".
The military deployed two Pakistani-produced unarmed surveillance drones in 2013. Analysts say Pakistan's drones look very much like drones from Pakistan's close ally, China.