Officials said the CIA-operated spy planes fired two missiles, with one hitting a house in the Tappi area about 20 kilometres east of Miranshah, the main town in North Waziristan tribal district.
The other missile hit a vehicle parked outside, reports said.
"The missile killed three people," an official was quoted as saying by local media reports.
The attack follows an October 11 attack in Orakzai agency, where at least 17 suspected militants were killed and more than 20 were injured when a US drone fired missiles at a compound in the Bulandkhel area.
After the October 11 attack in the tribal areas, Pakistan lodged a protest with the US embassy.
The al Qaeda-linked Haqqani network in North Waziristan, blamed for some of the deadliest attacks in Afghanistan, is one of the thorniest issues between Islamabad and Washington.
The attacks by unmanned US aircraft remain contentious with Pakistan saying it violates its sovereignty and fan anti-US sentiment, and American officials believing the strikes to be too important to be given up.
During the US Presidential debate yesterday, President Barack Obama and his Republican challenger Mitt Romney supported the drone strikes to kill terrorists.