A new education centre, transportation links and an upcoming visit by Afghan President Ashraf Ghani are all indicators of stronger bilateral relations.
Some students and parents are refusing to remove their headscarves, citing constitutional rights.
Recruiters from select US universities toured local schools and universities across Kazakhstan to talk with students about educational opportunities in the US.
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.