After coming through the youth categories of Red Star Belgrade, Stojanović went on numerous loans, having a breakthrough season at Bosnian club Leotar in 2002–03.
He was the team's top scorer with 22 goals in 23 league games,[1] helping them win their first national title in history.
[2] Following his return to Red Star, Stojanović played mostly as a substitute and scored several crucial goals in the 2003–04 season,[3] helping the side win the championship.
In January 2005, Stojanović was transferred to Belgian club Genk, signing a three-and-a-half-year contract.
In July 2018, aged 38, Stojanović agreed terms with Belgrade Zone League side Leštane.