Mullah Fazlullah, believed to have been operating from hideouts in the forests of eastern Afghanistan.
"I confirm that Mullah Fazlullah, leader of the Pakistani Taliban, has been killed in a joint air operation in the border area of Marawera district of Kunar province," Mohammad Radmanish, spokesman for Afghan defense ministry said on Friday.
This is not however the first time reports have emerged of the death of Fazlullah after the elusive chief of the banned group was named TTP chief in late 2013. He succeeded Hakimullah Mehsud who was killed in a drone strike in November of that year.
Later on Friday, the Pakistani army said that Afghan President Ashraf Ghani called Pakistani army chief Qamar Javed Bajwa to share the news of the Tehreek-i-Taliban Pakistan (TTP) leader's death.
"Killing of TTP commander is a positive development," the Pakistani army said in a statement.
"Pakistan military leadership has always maintained that a cooperative and coordinated approach is the best response to the menace of terrorism."
According to analysts, because Fazlullah was in Kunar, Islamabad continually accused Afghanistan of supporting groups that target Pakistan.