[1] He made his competitive debut for the club in the return leg of the UEFA Champions League second qualifying round, coming on as a substitute for Zvonimir Vukić in a 1–0 away win over Shkëndija on 19 July 2011.
[2] After missing the vast majority of the 2011–12 season due to mononucleosis, Ninković made his league debut in a 4–1 away victory against Rad on 31 March 2012.
[3] He became the club's youngest captain ever on 31 October 2012 at 17 years, 10 months and 12 days, coming on as a substitute in a 1–2 Serbian Cup loss to Borac Čačak, thus surpassing Stevan Jovetić.
On 1 February 2016, Ninković was transferred to Italian club Genoa, being immediately loaned to fellow Serie A side Chievo until the end of the 2015–16 season.
[17] On 25 October 2012, alongside Ognjen Mudrinski, Ninković received a one-year ban from the Football Association of Serbia following incidents after the game with England.