According to United Nations, the fighting has forced some students from their homes, while others can no longer attend school.
In Kunar province, many villages have been emptied of children, and several schools have been destroyed in the conflict.
A report by Agence France-Presse said the clashes have severely damaged schools as well as homes, leaving thousands of children without access to education.
The report said around 22 schools in Kunar alone have been damaged and require reconstruction.
Mohammad Amin Shaker, a school headteacher in Kunar, said children who had been studying are now out of school, and the school building has been destroyed.
Thousands of people have also been displaced and are now living in difficult conditions along the Kunar River.
One displaced resident said children are deprived of education and families are living in poor conditions in tents.
Displaced families have called on the international community for assistance.
United Nations Assistance Mission in Afghanistan said hundreds of civilians have been killed since the clashes began.
Islamabad accuses the Taliban of supporting anti-Pakistan groups and providing them shelter, claims the Taliban deny. The border regions between Afghanistan and Pakistan has remained tense for nearly two months.