Hafiz Saeed Khan -- a former Pakistani Taliban commander who hailed from Pakistan's tribal region -- was among 30 IS-linked cadres killed in the strike in the restive Nangarhar district, close to the Pakistani border.
Khan was in January appointed the chief of the radical Iraq-and-Syria based outfit, which is also known by its Arabic name Daesh, in Afghanistan and Pakistan, an area they call Khorasan.
"As a result of drone strike in Achin district on gathering place of Daesh, 30 people associated with Daesh including their leader Hafiz Seed were killed," it said.
The death of Khan could deal a major blow to the outfit's ambitions to establish a strong presence in Afghanistan and Pakistan.
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However, this is not the first time Khan has been reported killed. He was the second top rebel killed in drone strikes in three days.
Khan and Shahid parted ways with Pakistani Taliban last year with five other rebels, and announced their allegiance to IS in October.
At war with the Afghan government for nearly 14 years, the Taliban have warned the IS group to stay out of the region.
IS rebels are active in eastern provinces of Afghanistan, where they had a bloody clash with the Afghan Taliban last month.
The Afghan government has warned that the IS is making inroads into Afghanistan and is active in at least three provinces.