After retiring as a player, Miljanović enjoyed a brief spell as manager of Bosnian side Proleter Teslić in 2008. In 2010, he managed at the lowest level of Spanish football with Alfaz del Pi. On 15 January 2018, he became the manager of Superettan side Eskilstuna.[4]
On 24 August 2020, Miljanović was named manager of Bosnian Premier League club Mladost Doboj Kakanj.[5] Five days later, on 29 August, in his first game as manager, Mladost beat Olimpik in a league match.[6] He suffered his first loss as Mladost manager against Zrinjski Mostar two weeks later, on 12 September.[7] Miljanović left Mladost at the end of the 2020–21 season.[8]
On 18 August 2021, he became the new manager of Borac Banja Luka.[9] On 22 August 2021, in Miljanović's debut game as Borac manager, his team drew against Rudar Prijedor in a league match.[10] Seven days later, on 29 August, he recorded his first win as the club's manager, beating Radnik Bijeljina.[11] On 3 April 2022, Miljanović resigned as manager following a disappointing league draw against Rudar Prijedor the previous day.[12]
Shortly after, Miljanović became a part of Botev Plovdiv II's coaching staff. On 22 August 2022, he was appointed head coach of the team.[13] At the end of December 2022, he was appointed manager of FC Krumovgrad.[14]
During the rest of the season under Miljanović's helm Krumovgrad earned promotion to the top-tier of the Bulgarian league system. On 28 October, despite a somewhat successful start in the Bulgarian top-flight for Krumovgrad, Miljanović was replaced as manager.[15]
Personal life
Miljanović's son Daniel is also a professional footballer.[16]