As manager, Stojanović has won the Slovenian PrvaLiga twice, with Domžale, and the Serbian SuperLiga once, with Red Star Belgrade.

In September 2011, Stojanovič and Katanec were sacked after two successive defeats in the third round of qualifiers for the 2014 FIFA World Cup.

[5] On 24 June 2013, Stojanović replaced Ricardo Sá Pinto as a manager of Red Star Belgrade.

[citation needed] On 13 January 2016, Stojanović was appointed the new manager of Changchun Yatai, replacing Marijo Tot.

[10] After a spell with Riga FC, Stojanović was appointed at Bulgarian club Levski Sofia on 30 July 2018, replacing Delio Rossi.

[11] The term was short-lived, as he was released by the club on 21 January 2019, amid reports of an upcoming move to become head coach of the Latvia national team.