Saudi-born Adnan Shukrijuma was killed in the Shinwarsak area of South Waziristan tribal district.
“His accomplice and local facilitator were also killed in the raid,” said a statement by military’s Inter Services Public Relations.
Army said Shukrijuma was a member of the core al-Qaeda leadership and was in charge of its global operations.
During the raid, a soldier was killed and another injured.
Shukrijuma was among the five men indicted in the US over a 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.
The US has long said the Saudi native was a threat to America and put USD5 million reward for his capture.
In a 2003 report in the Washington Post said Shukrijuma as a possible terrorism organiser in the style of Mohamed Atta, the suspected ringleader of the September 11, 2001, attacks.
Following the killing of Shukrijuma, Chief of Army Staff General Raheel Sharif tweeted that all terrorists would be eliminated from Pakistan’s soil. “None will be spared.”
Pakistan military spokesman Major General Asim Bajwa tweeted: “Top al-Qaeda Comd Adnan Al Shukri Aljuma with his 1 companion killed by Pak Army raid in S Waziristan today.”
He also tweeted that five “terrorists” were also arrested during the raid.
Shukrijuma had moved to South Waziristan to from North Waziristan Agency due to the ongoing Zarb-i-Azb military operation, the ISPR statement said.
The comprehensive military campaign against foreign and local militants was launched a week after a brazen insurgent attack on the country’s busiest airport in Karachi in June.
The military say they have killed over 1,100 militants so far, with 100 soldiers losing their lives in the operation.
The mostly-lawless tribal areas that border Afghanistan have been a hideout for militants — including al-Qaeda and the homegrown Tehreek-e-Taliban Pakistan (TTP) as well as foreign fighters such as Uzbeks and Uighurs.
PTI