A security official said Farooq was among five people killed when two missiles fired from the drone hit a compound.
The compound was completely destroyed in the attack.
His killing came a day after Pakistani forces killed top al-Qaeda operative Adnan Shukrijuma in raid at a house in South Waziristan.
The chief of Al Qaeda's global operations, Shukrijuma was wanted by the US over a 2009 plot to attack the New York subway system.
Shukrijuma was among the five men indicted in the US over the plot to bomb New York's subway system under orders from Al Qaeda leaders in Pakistan.
The New York indictment links him to the Manhattan plot and a similar never-executed scheme to attack British subways, according to media reports.
North Waziristan has long been used as shelter by the Taliban and Al Qaeda-linked militants and has frequently been targeted by US drones.
The Pakistani military launched a major offensive in North Waziristan in June and say they have killed more than 1,000 militants so far.
For almost a decade, American drone strikes in Pakistan's tribal belt have been deeply unpopular with the public.
Pakistani officials have publicly condemned the drone strikes, saying they violate sovereignty.
Al Qaeda's global operations chief killed in Pak army raid
6 militants killed in US drone attack in Pakistan
Aam aadmi should also be able to fly business class: Kejriwal
'Modi is a human being and human beings want to do good'
Shiva secures 25th place in maiden Luge World Cup finals