Hashim Thaci said in a statement on Wednesday that Kosovo's Intelligence Agency "successfully located, found and returned" the boy. He said the operation was "complicated and dangerous." It was authorized by Thaci and the country's President Atifete Jahjaga.
The boy was taken to Syria in June 2014 by his father Arben Zena against his mother's will. No other details were immediately available.
Hundreds of Kosovo Albanians have joined the ranks of Islamic militants in Syria and Iraq in recent years.
Kosovo is secular but its population of some 1.8 million is overwhelmingly Muslim.