[6] After the club suffered relegation from the top flight, Milanović continued managing the team in the Second League until January 2004.
[7] In June 2009, Milanović was named as new manager of Laktaši in the Premier League of Bosnia and Herzegovina,[8] but left the club before the end of the year.
In July 2014, Milanović took charge as manager of Serbian SuperLiga side Rad,[10] returning to the club after a decade elsewhere.
[11] In August 2016, Milanović became manager of Zemun for the second time,[12] guiding them to a second-place finish in the Serbian First League and promotion to the top flight after 10 seasons.
[13] In June 2019, Milanović was appointed as manager of Kazakhstan Premier League side Irtysh Pavlodar.