Zawahiri provided "strategic guidance" to the group's global network and played a key role in the 9/11 attacks that killed almost 3,000 people in 2001, a decade before he took over leadership of the terrorist group.
Until his death, the US government was offering a reward of up to $25 million to anyone with information on his whereabouts.
So how did Ayman Al Zawahiri go from a rich Egyptian child to a terrorist leader?
Path to radicalism
On June 19, 1951, Ayman Mohammad Rabi Al Zawahiri was born in Giza, Egypt to an affluent and politically well-connected family.
His paternal grandfather, Sheikh Al Ahmadi Al Zawahiri was Imam of the prestigious Al Azhar mosque. His father was a pharmacology professor at the Ain Shams University of Cairo.
Zawahiri's grand-uncle, Abdul Razzaq Azzam was the first secretary general of the Arab League, US Lieutenant Commander Youssef H Aboul-Enein wrote in a 2004 report on Zawahiri.
All this should have lined Zawahiri up for a privileged childhood and a glittering career, but Egypt's 1967 war with Israel was the catalyst that sent him in a criminal direction.
"After being swept up by [Jamal Abdel] Nasser’s wave of Arab nationalism, the crushing defeat sent many Egyptians searching for answers, and a few like Zawahiri found it in Islamic radicalism," Lt Com Aboul-Enein wrote.
Zawahiri went on to study medicine, and was awarded a master's degree in surgery.
1981: Sadat assassination
Zawahiri was arrested on suspicion of being involved in the 1981 assassination attempt of Egyptian president Anwar Sadat, but was later acquitted of the charges and served only three years for illegal possession of firearms.
"His stay in prison only increased his militancy," Stephen E Atkins wrote in his book The 9/11 Encyclopedia.
In the pages of a book by Muslim Brotherhood leader Sayyed Qutb, Zawahiri found a spark that lit his bloody path ahead.
After his release from prison, Zawahiri took over the Egyptian Islamic Jihad (EIJ) group, which he helped found while a medical student. The group was involved in numerous anti-government attacks and assassination attempts.
In 1985, Zawahiri went to Saudi Arabia, where he practised medicine for a year in Jeddah.
He then moved to Pakistan to get closer to the war against the Soviets in Afghanistan.
In 1986, Zawahiri met bin Laden and became his "personal adviser and physician", Mr Atkins wrote.
Zawahiri is believed to have had a great influence on bin Laden.
"Zawahiri managed to introduce drastic changes to Osama bin Laden's philosophy ... mainly because of the friendship that developed between them," Montasser Al Zayyat wrote in his book The Road to Al Qaeda: The Story of Bin Laden's Right Hand Man.
"Zawahiri convinced bin Laden of his jihadi approach, turning him from a fundamentalist preacher whose main concern was relief work, into a jihadi fighter, clashing with despots and American troops in the Arab world."
Zawahiri's group was linked to a massacre in Luxor, the tourist destination in Egypt, in which 58 western tourists and four Egyptian security guards were killed.
"This terrorist act was so brutal that it caused a backlash in both Egyptian public opinion and among the leadership of the Egyptian Islamic Jihad," Mr Atkins wrote.
1998: US embassies
Zawahiri was indicted for his role in the 1998 bombings of two US embassies, in Kenya and Tanzania, that killed 224 people, including Muslims, and wounded 5,000 others.
That was also the year that the threat of Al Qaeda, bin Laden and Zawahiri became known on an international scale, after Zawahiri's EIJ officially merged with Al Qaeda.
1999: Al Qaeda designated a terror organisation
The US State Department officially designated Al Qaeda as a Foreign Terrorist Organisation (FTO).
2000: USS Cole bombings
On October 12, 2000, the USS Cole American navy destroyer was being refuelled in the port of Aden, Yemen. Two men in a small motorised rubber dinghy pulled up to the ship and blew themselves up, killing 17 sailors and injuring more than 30 others.
Zawahiri is believed to have plotted the attack.
2001: 9/11 attacks
A year later, Zawahiri was identified as co-ordinator of the September 11 attacks of 2001 when two hijacked jetliners flew into the World Trade Centre in New York and a third hit the Pentagon, killing almost 3,000 people.
In a 21-chapter book that he wrote after the attacks, Zawahiri revealed Al Qaeda's wider goals, and blamed the "Arab and western media" for "distorting" the image of Arabs, Afghans and Muslims and the role they played in fighting the Soviet Union.
He also explicitly said that the group's role is to "seek revenge against the gang-leaders of global unbelief in the US, Russia and Israel".
Since the US invasion of Afghanistan after the September 2001 attacks, Zawahiri was elusive. Although he was almost captured several times, his exact whereabouts remained largely unknown.
He most recently made a brief appearance in a video released this year commending a Muslim Indian student who protested in defence of the hijab.