Cross-border tensions escalated following a string of suicide bombings in Pakistan.
The reported toll adds to fears of a renewed cycle of retaliation between the neighbors, threatening a fragile ceasefire along their 2,600-km (1,600-mile) frontier and further straining ties as both sides trade blame over militant violence.
The United Nations Assistance Mission in Afghanistan said it had received "credible reports" that overnight Pakistani airstrikes on February 21-22 killed at least 13 civilians and injured seven in the Behsud and Khogyani districts of Nangarhar province.
Separately, Taliban spokesman Zabihullah Mujahid earlier reported dozens killed or wounded in the strikes, which also hit locations in Paktika province.
Reuters could not independently verify the reported toll.
Pakistan said it launched the strikes after blaming recent suicide attacks, including during Ramadan, on militants operating from Afghan territory.
In a post on X, Pakistan's information ministry said the "intelligence-based" operation struck seven camps of the Pakistani Taliban and Daesh (ISIS or ISIL) Khorasan Province.
It said it had "conclusive evidence" the militant assaults on Pakistan were directed by "Afghanistan-based leadership and handlers."
Kabul has repeatedly denied allowing militants to use Afghan territory to launch attacks in Pakistan.
The strikes took place days after Kabul released three Pakistani soldiers in a Saudi-mediated exchange aimed at easing months of tensions along the border.
Afghanistan's defense ministry condemned the strikes and called them a violation of sovereignty and international law.
It said an "appropriate and measured response will be taken at a suitable time."
The Afghan foreign ministry said it had summoned Pakistan's ambassador.
Additionally, in a statement on the February 21-22 strikes, Afghanistan's education ministry said eight school students, five boys and three girls, were killed in Behsud in Nangarhar province.
It added that one madrasa student was injured in Barmal in Paktika province, dozens of other civilians were killed or wounded and educational centers destroyed.
Reuters said it could not independently verify the information.
The latest strikes follow months of clashes and repeated border closures that have disrupted trade and movement along the rugged frontier.