2015–17: Arrival and league champions

Ninković made his debut as a substitute in a 2–1 away loss against Adelaide United in the FFA Cup on 26 August.^[11] On 10 October, he made his league debut at home in a 1–1 draw against Melbourne City.^[12] Two weeks later, Ninković scored his first goal in the tenth edition of the Sydney Derby, scoring the winning goal in a 1–0 win against Western Sydney Wanderers.^[13][14] He added his second and third goals of the season on 2 January 2016 with two goals against Melbourne City in a 2–2 draw at AAMI Park.^[15][16] In March, Ninković was taken off in the first half after receiving an ankle injury during a match against Wellington Phoenix.^[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.^[18][19] On 5 April, he scored the only goal in a crucial 1–0 win against Pohang Steelers in the AFC Champions League group stage.^[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.^[21] Five days later, he scored a brace after coming off the bench in a 4–0 win against Perth Glory in the final round of the competition.^[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).^[25][26] His performances in October led his side unbeaten in five matches and awarded him the PFA A-League Player of the Month.^[27][28] On 13 November 2016, Ninković scored two goals and assisted one to win 4–1 against Perth Glory.^[29] His performance and consistensy against Perth received praise from former Socceroo Mark Bosnich who said, "He is a phenomenal player but I think the most important thing this season is he's actually been showing it week in, week out".^[30] On 30 November, Ninković played in his first final, since joining Sydney FC, losing 1–0 against Melbourne City in the FFA Cup.^[31] Four days later, he scored his fifth goal of the season against Newcastle Jets.^[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.^[33][34] On 1 April, Ninković was awarded the Alex Tobin Medal, being voted the best player from Fox Sports Australia after accumalating 11 Man of the Match awards during the season.^[35][36] On 15 April, Ninković scored a goal in a 2–0 against Newcastle at Allianz Stadium to win the Premiership for his side, the first they have won since 2009–10. Additionally, his side broke a league record after amassing 66 points in the league – beating Ange Postecoglou's Brisbane Roar side by a point.^[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.^[38] On 7 May, he achieved a double with Sydney FC, winning the Grand Final against rivals Melbourne Victory, via a penalty shootout with Ninković scoring the decisive penalty.^[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.^[41][42] On 10 May, he was awarded the A-League Players' Player of the Year and Members' Player of the Year award – becoming the third player in Sydney FC to have won three awards in a season after Miloš Dimitrijević and Matthew Jurman.^[43] He was one of the six Sydney FC players named in the PFA team of the season.^[44]

2017–18: Rise to a Sydney FC legend

Ninković began the 2017–18 season as a new marquee player for Sydney FC in the FFA Cup. He opened the campaign by scoring a goal in an 8–0 away win against Darwin Rovers, setting a new record in the competition.^[45][46] Ninković started in the remaining games as Sydney FC advanced to the finals against Adelaide United, who beat them the last time they met in a cup final. On 21 November 2017, the game commenced with Ninković opening the scoreline 1–0, putting it past Paul Izzo. The score drew level by Nikola Mileusnic, leading the game into extra time before Bobô scored the winning goal in the 110th minute.^[47] Ninković earned his third accolade with Sydney FC as the club won their first cup title in their history.^[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, skilfully beating four defenders and chipping the ball past Glen Moss to tie the game 1–1.^[50] The final score at Allianz Stadium was 2–2.^[51] After the match, the goal would be dubbed by Fox Sports as a goal of the season contender, and received further praise from Mark Bosnich, saying, "An absolutely special goal by a special player and once again (he) came to Sydney's rescue".^[52] In March, Ninković missed on an AFC Champions League group match against Kashima Antlers due to hamstring problems.^[53] He returned to full fitness and scored his fifth goal of the season in a 2–1 defeat against Brisbane Roar.^[54] The week after, he scored a goal to win 2–1 against Central Coast Mariners, bringing his league tally to 6. 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.^[55]

On 13 April, Ninković celebrated his second consecutive premiership after a 1–0 win against Melbourne Victory in the final round of the A-League.^[56] At the end of the season, his performance and influence in Australian football received praises from many media and personnel including from Australian international Miloš Degenek who stated that "Ninkovic is the most appreciated footballer in Australia. [His arrival is] the best thing that happened to Australian football," adding "He has given Australia more than Alessandro Del Piero!".^[57] On 31 May, he extended his contract for two years with Sydney FC following the departure of Graham Arnold.^[58]

2018–20: Hyundai A-League Great

Under the system of inexperienced manager Steve Corica, the 2018–19 season saw the departure of key starters, Adrian Mierzejewski and Bobô leaving Ninković as the only marquee and foreign import at the club.^[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.^[61] After a quiet first half of the season with his side staying third place, Ninković scored his first goal of the season in the Big Blue losing 2–1 at AAMI Park on 26 January 2019.^[62] By February, he accumulated 21 key passes, with 6 assists and scored 1 goal.^[63] Although he later expressed his fustration for the lack of goals he scored during the season.^[64] On 6 April, Ninković scored the winning goal in a 2–1 Big Blue derby win against Melbourne Victory, shooting past Matthew Acton, after a cut back pass from Siem de Jong.^[65] After finishing second in the league below Perth Glory, Ninković scored a brace against Melbourne Victory in the semi final, contributing to a 6–1 win, the biggest win in the history of the Big Blue rivalry.^[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.^[67] At the end of the match, Ninković was awarded the Joe Marston Medal, recognising his performance in the Grand Final.^[68] He ended his 2018–19 campaign with 3 league goals (all against Melbourne Victory), the lowest he scored in a season with Sydney FC.^[69]

On 7 August 2019, Ninković injured his ankle during a match in the FFA Cup against Brisbane Roar, suspecting it was a broken ankle.^[70] He returned to training 5 days later, only missing a friendly match against Wollongong Wolves.^[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.^[72]

On 26 October 2019, Ninković started in the first Sydney Derby match of the season in front of 28,519 people, losing 1–0 to Western Sydney Wanderers at Western Sydney Stadium.^[73] The match would be a shock to many including Ninković as Wanderers broke a 980 days winless drought against the Sky Blues.^[73] Despite the loss, Ninković was award the Under Armour Man of the Match, creating 3 key passes and having a pass completion of 87.9% out of the 58 passes played during the game.^[74] On 17 December, he extended his contract for two years, rejecting a multi-deal offer from expansion side Macarthur FC.^[75] During an interview, Ninković opened up about the Macarthur transfer saying he was nearly close to signing. The offer was said to be a three-year deal with an opportunity for a coaching role at the end of his career.^[76] Further reports say that he was offered a $500,000 salary by Sydney FC before Macarthur offered a two-year deal with an option for a third, earning $750,000 per year.^[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.^[78] By April, Ninković scored 5 goals and assisted 3 (out of 31 key passes) from the 21 games he has played.^[79] Following a poor run of form, Ninković would claim his Premiers medal after a 2–1 loss against Western United in August.^[80] On 26 August, he scored in the semi final against Perth Glory, to open the scoring of the match. The final score was 2–0 at Western Sydney Stadium.^[81] The win was their first in 40 days with Ninković applauding his teammates for their efforts.^[82] He started in the Grand Final against Melbourne City, playing the full 120 minutes of the match when his side won 1–0 in extra time and claiming their fifth Grand Final win.^[83] Ninković was voted second in the Johnny Warren Medal with 28 points, falling short to Western United player Alessandro Diamanti (34 points).^[84]

2020–22: Last season

On 30 January, Ninković started his 2020–21 season, scoring his first goal by dribbling through four players, in a 3–0 win, against Macarthur FC in their inaugural season.^[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.^[86] This would be the Sky Blue's first win against the Wanderers since 15 December 2018.^[87] On 23 June, Ninković was awarded his second Johnny Warren Medal, sharing it jointly with Wellington Phoenix's Ulises Dávila – becoming the first players to share the award.^[88][89] Following a calf injury that made him miss the semi final win against Adelaide,^[90] Ninković came off the bench in the 72nd minute in a 3–1 Grand Final loss against Melbourne City on 27 June.^[91]

On 25 January 2022, Ninković scored in a 2–2 Big Blue derby against Melbourne Victory.^[92] On 26 February, he scored his second of the 2021–22 season in a 2–1 loss against Melbourne City.^[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.^[94]

On 4 June, Sydney FC released a statement on contract discussions with Ninković following a video he posted on Instagram, saying he would be leaving the club after his contract expires.^[95][96] On 21 June, the club officially announced the departure of Ninković.^[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. It has always been our intention for Milos to finish his playing career with Sydney FC. Despite our best efforts, Milos has decided to move on and we thank him for the major contribution he has made to our club."^[97]

Following his departure, Steve Corica stated his desire to retain Ninković even after his request to play off the bench, but only if Ninković obtained Australian citizenship so he could bring in new foreign signings. Corica made it clear that Ninković was only released due to his refusal to pursue citizenship.^[98] Ninković denied these claims made by Corica, in an interview with Code Sports. During the interview, he opened up about the situation with him and Corica, saying that Corica demanded he take up citizenship by the end preseason or "he had to retire" adding, "it will ruin his legacy".^[99] Ninković expressed his feeling of the situation stating, "I felt disrespect, I felt really bad that my career will depend on if I get the citizenship or not. That means if I get the citizenship I can play if I don't get the citizenship I have to retire".^[100]