After passing through the youth categories of Radnički Niš and Partizan, Mrdaković moved abroad to Belgian club Anderlecht at the age of 16. He played for their youth and reserve teams, before going on loan to fellow Belgian First Division side Eendracht Aalst in early 2002. Following an unsuccessful spell in Belgium, Mrdaković returned to his homeland and joined OFK Beograd on a free transfer. He became the team's top scorer in the 2002–03 season, bagging 20 league goals in 32 appearances. In August 2003, Mrdaković was transferred back to Belgium, penning a four-year contract with Gent. He left the Belgian club by mutual agreement in April 2004 and returned to OFK Beograd to finish the season. In early 2005, Mrdaković signed with Austria Salzburg. He left six months later for Ukraine and spent a little over a year at Metalist Kharkiv. In August 2006, Mrdaković signed with Israeli club Maccabi Tel Aviv. He made 36 appearances and scored eight goals across all competitions throughout the season. Over the next 12 months, Mrdaković played for Portuguese club Vitória Guimarães with similar success. In July 2009, Mrdaković returned to Europe and signed a two-year contract with Cypriot club Apollon Limassol. He failed to make an immediate impact, appearing in just one game, and was loaned to fellow Cypriot First Division side Ethnikos Achna in the 2010 winter transfer window. Until the end of the season, Mrdaković scored eight goals in 14 appearances. He subsequently returned to Apollon Limassol and became the league's top scorer in the 2010–11 campaign with 21 goals. In June 2011, Mrdaković signed with AEK Larnaca on a three-year deal. He scored seven times in 18 league games, before leaving the club in February 2012. In early 2012, Mrdaković signed with Chinese Super League club Jiangsu Sainty, thus returning to China after spending three seasons in Cyprus. He appeared on five occasions and scored once in a little more than 70 minutes of action. Less than a year after leaving for China, Mrdaković returned to Cyprus and joined Enosis Neon Paralimni to recover the form in the remainder of the season. In July 2013, Mrdaković moved to Super League Greece side Veria. He made 13 appearances and scored five goals in the top flight. In January 2014, Mrdaković joined Tampines Rovers of Singapore as their marquee player. He scored a career-high 25 goals in all competitions, helping the side win two cup titles. In February 2015, Mrdaković returned to Greece and signed with Levadiakos. He appeared in just three games in the Super League, but failed to score in the process. In June 2015, Mrdaković signed with Vojvodina for one year. He scored two goals in the qualifiers for the 2015–16 UEFA Europa League, as they were eliminated in the play-off round. In January 2017, Mrdaković returned to OFK Beograd, stating his intention to retire at the club.
