The unmanned CIA-operated spy plane fired two missiles at the compound in Mirali region of North Waziristan this evening.
Six persons were killed in the attack, state-run Radio Pakistan reported.
On Saturday, three suspected militants were killed when a drone targeted a vehicle in North Waziristan Agency.
The US has continued its drone campaign in the tribal belt bordering Afghanistan despite strong protests from Pakistan.
During a meeting with US Special Envoy for Afghanistan and Pakistan Marc Grossman on September 15, President Asif Ali Zardari reiterated Pakistan's call for an end to drone attacks.
Zardari described the use of drones as counter-productive in the fight against militancy and in the "battle of winning hearts".
He said Pakistan and the US need to find alternatives to drones.
Today's drone strike occurred hours after Zardari met US Secretary of State Hillary Clinton in New York. Zardari is visiting the US to attend the UN General Assembly session.
