The CIA-operated spy planes fired four missiles at the compound in Degan area of North Waziristan, officials were quoted as saying by TV news channels. The area is considered a stronghold of Taliban and Al Qaeda elements.
Six suspected militants were killed inside the compound when it was struck by missiles.
The new drone attacks come on the heels of a volley of strikes by the pilotless planes in the area over the past two weeks in which Badruddin Haqqani, the operational commander of the Haqqani network was reportedly killed.
On August 24, US drones carried out three attacks that killed at least 18 militants despite a protest by the Pakistan government just a day earlier.
Nearly 40 militants were killed in drone strikes last month.
Pakistan`s Foreign Office summoned a senior US diplomat last month to protest the drone strikes, describing them as unlawful and a violation of the country?s sovereignty.
"It was emphatically stated that such attacks were unacceptable," the Foreign Office spokesman said at the time.