Akhundzada joined the Taliban in 1994 and became one of its early members. He played various roles within the organization, including serving as an instructor at a seminary and later becoming the head of the group's council of religious scholars.

After the fall of the Taliban government in 2001, Akhundzada became the head of the group's council of religious scholars. He was responsible for issuing fatwas and advising the leadership on religious matters.

During a 2012 lecture by Akhundzada, a man attempted to shoot him, but the pistol jammed. The Taliban accused the Afghan intelligence agency of the attempted shooting.

In May 2016, Mullah Hibatullah Akhundzada was elected as the supreme leader of the Taliban, succeeding Akhtar Mansour. He is known for his religious leadership and issuing fatwas within the Taliban.

Akhundzada's younger son Abdur Rahman Khalid died carrying out a suicide attack on an Afghan military base in Girishk in Helmand Province. Taliban officials said that Akhundzada was aware of his son's intention and approved of it.

Under the leadership of Akhundzada, Taliban won the Battle of Darzab by defeating the Islamic State of Iraq and the Levant's Khorasan branch.

There were rumors about the death of Mullah Hibatullah Akhundzada in 2020, but the Taliban denied these claims. The uncertainty surrounding his status led to concerns about potential factionalization within the Taliban.

In May 2021, Akhundzada called the Afghan people to unite for the development of an Islamic state once the United States forces withdraw.

Forces under Akhundzada's nominal command began a general offensive seeking to achieve a final victory in the war. During his leadership, the United States troops withdrew, and the Taliban gained control of Kabul.

Akhundzada is seen as a religiously ultraconservative figure and ideologue within the Taliban. He is said to oppose girls' education in Afghanistan, vetoing a plan to return girls to secondary education by March 23.