[1] In December 2012 it was announced that the last six months of Ninković's contract, which expires in June 2013, was to be spent on loan with French club Évian.

[2] Ninković initially was negotiating a transfer to Red Star Belgrade, but was denied the possibility to shorten his contract with Dynamo from June 2013 to January 2013.

[17] The injury was expected to leave him out for the rest of the season but after only two weeks due to an extensive rehabilitation program, he made his return against Brisbane Roar.

[20] The win secured Sydney FC's position at the top of the group, leading them to qualify for the knockout stages for the first time in the club's history.

[22] Ninković finished his debut season notching 5 assists (creating 29 key passes) and scoring 4 goals for Sydney FC.

[23] Building on his form the following season, Ninković scored two goals and provided two assists in five appearances, netting against Wellington Phoenix (1–0),[24] and Newcastle Jets (2–0).

[30] On 30 November, Ninković played in his first final, since joining Sydney FC, losing 1–0 against Melbourne City in the FFA Cup.

[32] In January 2017, Ninković continued his excellent form, scoring a goal against last season reigning double winners Adelaide United and assisting Filip Hološko to win The Big Blue derby to increase his side's unbeaten run to 17.

[37] For his contributions and performances for his side, Ninković was awarded the Johnny Warren Medal (the first Sydney FC player to do so) with 9 goals and 11 assists to his name.

[39] After speculation of leaving, possibly to move back to Serbia,[40] Ninković was re-signed as a marquee player for an annual salary of $1,300,000, replacing Filip Hološko who later departed.

[48] Ahead of the league season, Ninković utilised his playmaking skills, forming a partnership with new arrival Adrian Mierzejewski who added more to the attack with Alex Brosque and Bobô.

[49] On 3 January 2018, he scored a goal against Newcastle, skillfully beating four defenders and chipping the ball past Glen Moss to tie the game 1–1.

[52] In March, Ninković missed on an AFC Champions League group match against Kashima Antlers due to hamstring problems.

On 3 April, he scored the opening goal in a crucial AFC Champions League match against Suwon Bluewings that ended with Sydney FC winning 4–1.

[60] Whilst also applying for permanent residency in October, he was partnered in midfield with new loan signing Siem de Jong and formed a partnership in the attack with Adam Le Fondre.

[66] Ninković started in the Grand Final, against Premiers' winner Perth Glory, where his side eventually won on penalties, bringing him his second championship to Sydney.

[71] Ninković scored two goals in a friendly match against newly founded club Western United, netting in the 25th and 71st minute to end the game 2–1.

[77] The transfer brought much dislike between the clubs, and in response, Sydney FC would raise the minimum ticket price to $50 for the away section in their first match against the Bulls in January 2021.

[76] On 31 January 2020, Ninković was left out of the squad's 2020 AFC Champions League campaign due to the foreign limit for non-Asian players.

[85] On 23 May, Ninković assisted the only goal, a precise lob pass for Bobô who volleyed it in the net, to win 1–0 against Western Sydney Wanderers.

[93] However, after an investigation by Australian Professional Leagues (APL), the scoreline was changed to 3–0 in favour of City due to insufficient U23 players in the Sydney FC squad while Ninković's goal still counted towards his goalscoring tally.

[97] Sydney FC Chief Executive Officer Adam Santo spoke about his departure saying:"Milos is a legend of our club and we spent a number of weeks talking to him, in the hope he would continue to play a role in our future.

We were optimistic he would accept our offer to continue playing and remain at the club long term, where he would transition into full time employment.

[100] It was announced on 3 July 2022 that Ninković had joined arch rivals the Western Sydney Wanderers, signing a one-year deal, ahead of the upcoming season.

TRAITORS' LEGACIES WILL PERISH', along with depictions of club greats Steve Corica, Rhyan Grant and Alex Brosque as knights in shining armour, with Ninković's old No.