Already struggling with the rise of rival terrorists from the ISIS group, al-Qaeda has suffered a series of setbacks in recent months with several commanders reported killed, AFP reports.
In a video statement, Al-Qaeda in the Arabian Peninsula confirmed that Nasir al-Wuhayshi was dead.
Wuhayshi "was killed in a US drone attack that targeted him along with two other mujahedeen", who were also killed, said the statement read by prominent al-Qaeda militant Khaled Omar Batarfi and dated June 15.
AQAP is believed was behind deadly attack on French magazine Charlie Hebdo in Paris earlier this year - said it had named its military chief Qassem al-Rimi as its new leader.
US officials were earlier reported to have been reviewing intelligence to confirm that Wuhayshi was killed in a CIA drone strike on June 9.
A local Yemeni official had told AFP that Wuhayshi was believed to have been killed in the raid in Al-Qaeda-held Mukalla, in southeastern Yemen.
A former aide to bin Laden, Wuhayshi attended the group's Al-Farouk training camp in Afghanistan in the late 1990s.
He is said to have fled Afghanistan in 2002 to Iran, where he was arrested and handed over to Yemen.
He was held there without charge until he escaped by tunneling his way out of prison with 22 others in February 2006.
In 2007, Wuhayshi was named head of AQAP, which Washington considers al-Qaeda's deadliest branch.
As well as the Charlie Hebdo attacks that left 12 people dead, AQAP was also behind an attempt to blow up a US commercial airliner on Christmas Day 2009.
Washington has repeatedly targeted AQAP militants in drone strikes in Yemen and killed several commanders in recent months, including Nasser bin Ali al-Ansi.
AQAP consolidate their grip on Hadramawt province and its capital Mukalla, a city of more than 200,000.