Born in Brus, Milisavljević made his first senior appearances with Radnički Niš in 2002. He spent three seasons at the club, before transferring to OFK Beograd in the summer of 2005. Six months later, Milisavljević returned to Radnički Niš.
In the 2007 winter transfer window, Milisavljević moved abroad to Macedonia and joined Rabotnički. He helped them win the double in the 2007–08 season. Afterwards, Milisavljević switched to fellow Macedonian club Vardar.
In the 2009 winter transfer window, Milisavljević was transferred to Romanian side Vaslui. He spent the next three and a half years there, before moving to fellow Liga I club Rapid București. In early 2013, Milisavljević signed with Bulgarian champions Ludogorets Razgrad. He also played for CSKA Sofia and Beroe Stara Zagora.