Since retiring he has acquired a UEFA Professional Coaching Licence in Germany and in 2003 started his manager career when he became assistant manager of the Lithuanian national team. The same year Ivanauskas also took caretaker position in FK Vėtra, and was later appointed on a permanent basis. In the 2004 season, Ivanauskas led FK Vėtra to its first ever Intertoto Cup third-round appearance, eliminating Tony Mowbray's revitalised Hibernian side, but resigned in August citing personal problems and that he was too occupied with his job in the national team. However, in just a couple of weeks time he took over at FBK Kaunas and led the club to Lithuanian championship title and Lithuanian Cup victory.