In March, the U.S. offered a $5 million reward for information on Fazlullah.
Afghan Defense Ministry spokesman Mohammad Radmanish told NBC News that Fazlullah died in a strike in the Marawaya district of the border province of Kunar.
Let our news meet your inbox. The news and stories that matters, delivered weekday mornings.
Earlier, Lt. Col Martin O’Donnell, a spokesman for U.S. Forces in Afghanistan, said in a statement that U.S. forces had carried out an airstrike Thursday in Kunar "which targeted a senior leader of a designated terrorist organization."
Pakistan is considered key to persuading Afghan Taliban leaders, who Washington believes shelter on Pakistani soil, to open negotiations to end the 17-year-old war in Afghanistan.
Prior to the Afghan Defense Ministry stating that Fazlullah had been killed, several members of the Pakistani Taliban told NBC News they had been unable to make contact with him and other senior commanders since receiving word of the strike.
They said they feared four other top commanders may also have been killed.
"Most of our people are seriously concerned after they heard about the killing of our leader, but the top leadership is out of access," Pakistani Taliban commander Maulvi Obaidur Rahman told NBC News.
Like many other Pakistani militants, Khorasani had crossed into Afghanistan after the Pakistani army launched a major military offensive in the Swat Valley in 2009.
Mushtaq Yusufzai reported from Peshawar, Francis Whittaker from London, and Ahmed Mengli from Kabul.