Teachers are welcoming the subject matter, which is aimed at helping the younger generation act socially responsible.
The move will mainstream seminaries, preventing terror links and allowing the government to provide funds for new facilities, say officials.
More than 15,000 schools have been closed in the province due to various insurgent activities.
The programme is currently running at jails in Peshawar and Mardan. Authorities are looking to expand the programme even further.
The Pakistani government is offering special student visas, dedicated slots in schools and scholarships for Afghan students.
Education is the key to development and ending militancy and violence in the Federally Administered Tribal Areas, observers say.
Pakistani authorities are issuing special identification cards to Afghan schoolchildren residing along the border, enabling them to go to Pakistani schools.
Pakistanis want the government to ensure that seminaries disassociate themselves from extremism and teach pupils a variety of modern subjects.