Slovan Slaviša Stojanović started his manager career at the age of 29. Domžale He was appointed at Domžale in 2002. In his first year in charge, the manager promoted the team in the Slovenian PrvaLiga.
Celje Slaviša Stojanović signed for Celje in 2008.
In that season, his new team finished the Slovenian PrvaLiga with 3 points more than the champions from Domžale. United Arab Emirates national team In 2009, he took his job as assistant manager at the United Arab Emirates national football team
Stojanović helped manager Srečko Katanec qualify the squad for 2011 AFC Asian Cup. Stojanović as the assistant manager was sacked as well.
Slovenia national team On 24 October 2011, Slaviša Stojanović became the new manager of the Slovenia national team after the Football Association of Slovenia had had the contract with Matjaž Kek terminated by mutual agreement earlier that day.
On 9 December 2012, he resigned as the manager of the Slovenia national team Red Star Belgrade On 24 June 2013 he replaced Ricardo Sá Pinto as a coach of Red Star Belgrade. He lost his first game in Jelen Super Liga against FK Javor Ivanjica but in the end of first half-season he was just 1 point behind FK Partizan.
K. Lierse Saskatchewan On 5 September 2014 he replaced Stanley Menzo as a coach of Lierse South.K. He signed a contract until the end of the season.
On January 28 he resigned as manager for Lierse South.K. after bad results Manager of the year in the 005, 2006.