After completing his formation, Nikolić spent some time on loan with third-tier club Dorćol, before retiring from the game due to an injury.

He served as assistant manager to both Mihailo Ivanović and Aleksandar Janjić, eventually replacing the latter one on 26 October 2008, after the club earned just five points from the opening nine fixtures.

[1] Three days later, Nikolić became the youngest manager ever in the top flight of Serbian football, recording a 1–0 win over Vojvodina.

On 23 May 2011, two rounds before the end of the 2010–11 season, Nikolić secured a spot in the 2011–12 UEFA Europa League, but decided to leave the club due to "achieved goals".

[10] On 11 January 2016, Nikolić was presented as new manager of Slovenian club Olimpija Ljubljana, penning a two-and-a-half-year contract.

[11] He rejoined his countryman Ranko Stojić, the club's director of football, as they previously performed the same roles at Rad.

[12] On 10 April 2016, in a league fixture versus Zavrč, Nikolić reportedly called his player, Blessing Eleke, a "black idiot" for elaborately celebrating an injury-time equalizer in an eventual 1–1 draw.

However, the club was defeated by AEK Athens F.C., therefore, the cub was eligible to play in the group stages of the 2018–19 UEFA Europa League.

On 14 May 2020, the board of directors of Russian Premier League club Lokomotiv Moscow announced the signing of Nikolić, with contract beginning on 1 June 2020.