The 31-year-old midfielder joined the Christie Park club after moving to Aberdeen to be closer to family who are based there.
Kovacevic featured twice for his country's under-21 side when he played in Croatia with HNK Cibalia. He also had spells in Israel where he played for Bnei Yehuda Tel Aviv, Hapoel Ramat Gan and Macabbi Herzliya before returning to Croatia with NK Istra 1961 and NK Lucko.
Dave McGinlay, the Huntly manager, said: "I am pleased to sign Hrvoje. I think the people running this club should be applauded for helping to get this done."