During his managerial career, Milovanović worked at Mladost Lučani, Borac Čačak, Jagodina, Metalac Gornji Milanovac and Napredak Kruševac.
He subsequently took charge at Borac Čačak while the club participated in the 2008–09 UEFA Cup, being eliminated by Dutch side Ajax in the first round.
In early 2014, Milovanović returned to Mladost Lučani, helping them win the 2013–14 Serbian First League and gain promotion to the top flight.
They later finished in fourth place in the 2016–17 Serbian SuperLiga, securing a spot in the 2017–18 UEFA Europa League.
He was appointed as sporting director of Mladost Lučani in July 2019, thus leaving his managerial role after five and a half years.