Professional skills will help graduates of Islamic schools to find jobs and protect them from radicalisation, observers say.
In addition to a successful pilot program, Kyrgyz officials plan to adopt a History of Religious Culture textbook in all schools starting in 2018.
Authorities are counting on the elderly and experienced to counsel the younger generation.
'This is a major, badly needed and timely contribution,' said one Kyrgyz official.
Some parents in Kazakhstan still try to send their children abroad, but outreach by the government is making them think twice.
Young Kazahstanis studying abroad can become an easy target for terrorist recruiters, warn officials and clergy.
Authorities are acting on concerns about the influence of radical movements.
The coming reforms come after complaints about the previous system split students from their familiar environment after 9th grade.
Enrolling university students from other Central Asian countries will help foster regional co-operation and prevent youth radicalisation in Central Asia, predict observers.
Thousands of Kazakhstani high school students in Pavlodar Province participated in an online conference on countering extremism and terrorism.