Relations between the former allies have remained strained since February, when the two sides fought their worst clashes in years.
The dispute centres on militancy in Pakistan, with Islamabad accusing Kabul of harbouring militants who stage cross-border attacks from Afghan territory.
Afghanistan's Taliban government denies the charges and says militancy is Pakistan's internal problem.
The airstrikes on Monday came days after a police facility in northwest Pakistan was attacked, killing at least 16 people.
At least one house in Kunar province was hit in the strikes, killing three members of the same family and injuring four others, Taliban deputy spokesperson Hamdullah Fitrat said in a post on X.
"In Barmal District of Paktika (province), two locations...were bombarded, destroying one shop and one unoccupied house, with no casualties reported," he said.
Pakistan's military did not immediately respond to a request for comment.
Afghanistan had launched drones against Pakistan in July, which Islamabad had said its forces had intercepted and shot down.
The worst single incident occurred in March, when more than 400 people were killed in a Pakistani airstrike on Kabul, which the Afghan Taliban said targeted a drug rehabilitation centre.
Islamabad denied the charge, saying it "precisely targeted military installations and terrorist support infrastructure".
Pakistan has a large air force, with 422 combat aircraft and more than 260 helicopters, according to data from the London-based International Institute for Strategic Studies.
Afghanistan has no fighter jets but is known to possess at least six aircraft and 23 helicopters, and drones that have previously been used in fighting with Pakistan.
