[4] At the beginning of 2016, he joined the first team of Partizan under coach Ivan Tomić and signed a five-year contract, but also stayed with Teleoptik on dual registration until the end of season.

[10] Milenković started new season pairing with Cédric Gogoua for the second qualifying round of the 2016–17 UEFA Europa League against Zagłębie Lubin.

After several bad results and some injuries of the players in defense, Milenković started playing continuously from the fourth fixture against Javor Ivanjica onwards.

However, the tragic death of the team captain Davide Astori made Pioli change his mind and include Nikola in the starting eleven more often.

[24] After another corner combination between Pulgar and Milenković, the Serbian international scored the equalizing goal in his side's 2–1 defeat against Roma at the Stadio Olimpico.

[25] At the end of the 2021–22 Serie A season Fiorentina finished in seventh position and secured their first participation in the UEFA Europa Conference League.

[26][27] On 18 July 2024, Milenković signed for Premier League side Nottingham Forest on a five-year deal for an undisclosed transfer fee,[28] believed to be around £12 million.

[29] Milenković debuted on 24 August 2024, as Nottingham Forest claimed their first win of the 2024/25 campaign by beating Southampton 1–0 at St Mary's Stadium.

[33] Later the same year, he was called up to the Serbia U20 national squad by coach Nenad Lalatović, and made his debut for the team in a match against Montenegro.

In June 2018, Serbian head coach Mladen Krstajić included Milenković in the final 23-man squad for the 2018 World Cup.