"In an intelligence-borne operation, top al-Qaeda leader Adnan El Shukrijumah was killed by the Pakistan Army in an early morning raid in Shinwarsak, South Waziristan, today," the army statement said on Saturday.
It added that Shukrijumah, 39, was killed along with his accomplice and local facilitator in a hideout compound in Shinwarsak.
The Saudi-born militant has been described by the Federal Bureau of Investigation (FBI) as "one of the leaders of al-Qaeda's external operations program" for his attempts to blow up the New York subway system in 2009 and plots connected to targets in the United Kingdom.
The FBI had offered a $5 million reward for the capture of the terrorist.
The Pakistani military launched a major offensive in North Waziristan in June and says it has killed more than 1,100 militants so far, with 100 soldiers having lost their lives in the operation. A variety of militant groups used the bases there to stage fatal attacks in both Afghanistan and Pakistan.
North Waziristan is considered a stronghold of pro-Taliban militants in Pakistan.
The militants have carried out numerous attacks against Pakistani security forces and civilians, and managed to spread their influence in various regions of the country despite sporadic offensives by the Pakistani army.
Thousands of Pakistanis have lost their lives in bombings and other militant attacks since 2001, when Islamabad entered an alliance with Washington in the so-called war on terror.