The government confirmed that Abdul Hasib had been killed
Hasib was killed in an operation led by Afghan special forces in the eastern province of Nangarhar, President Ashraf Ghani announced.
He was appointed last year after his predecessor Hafiz Saeed Khan died in a US drone strike and is understood to have ordered a series of high profile attacks.
One was on the main military hospital in Kabul in March by a group of militants dressed as doctors.
The US and Afghan forces, backed by drone strikes and other air support, have mounted a number of operations against IS this year in which dozens of fighters, mainly in Nangarhar on the Pakistan border.
Defeating IS in Afghanistan remains a top priority for the US which in April dropped its largest non-nuclear bomb on a network of caves and tunnels killing 94 fighters, including four commanders.
Additional reporting from IRN.