Rajkovic is an academy graduate of the Serbian club OFK, where he made his first team debut at the age of 15. In 2005, Chelsea bought Slobodan for 5 million euros, but he did not make a single appearance for the London club. Chelsea loaned him out for a number of years to different clubs like OFK, PSV, Twente and Vitesse. In 2011 Rajkovic moved to Hamburg. He made made 45 appearances for the club and scored two goals. In the 2015/16 season, Rajkovic played for Darmstadt and after he moved to Italy, where he spent the last four years playing for Palermo and Perugia.

Slobodan made his debut for the Serbian national team in 2008 and in total he played 19 matches.