The 17-year-old, who has signed a five-year deal, will spend next season with Barcelona B.
"This is a great day for me, I'm very happy. I'm a big fan of Barcelona, I have been all my life. I've watched Barca B this season and they've played great football," he told reporters.
Halilovic, who has already played for his senior national side, is widely regarded as one of the best young talents in European football.