After returning to OFK Beograd for a season, he moved to Hungarian National Championship club Videoton, where in 2003 he ended his professional career at the age of 29.

On 3 September 2008, he was appointed the head coach of Serbia national under-19 team that finished 3rd in 2009 UEFA European Under-19 Championship in Ukraine.

Within 24 hours, Stanojević was promoted as new Partizan head coach, and at the age of just 36 became the youngest manager in the club history.

[6] With Stanojević in position, Partizan won all seven remaining league fixtures, including the Eternal derby and defended the title.

Krstajić stated that he and Stanojević did not have full control over the sale and acquisition of players during summer transfer window, which affected the results on the field.

[9] Stanojević postponed his decision until 6 January 2012, when he confirmed he decided to continue his work as the head coach of Partizan.

[10] Despite this fact, the board of directors of Partizan dismissed Stanojević on 13 January 2012 and appointed Avram Grant as the new coach.

[12] On 4 April 2012, Stanojević was appointed as the new manager of Chinese Super League side Dalian Aerbin, replacing Chang Woe-ryong who resigned from the club the day before.

However, his coaching style was questioned by the club and the media of Beijing at the last months of the season, especially after losing to Guangzhou Evergrande in the semi-finals of FA Cup.

Under Stanojević the team reached semi-final of Toto Cup, after winning first place in group phase of competition.

On 15 September 2014 Maccabi Haifa started new season with first game at new Sammy Ofer Stadium in front of more than 27,000 supporters against Bnei Sakhnin F.C.

Despite the fact that Stanojević signed a three-year contract,[18] he was relieved of his duties on 11 August 2017, almost two months later, as said from the club mainly due to poor performances and issues of squad management and harmony.

In this season Stanojević lead Partizan to Serbian Cup final where his team was defeated by Red star after penalties.

Also, Partizan for the first time plays in Europa Conference League reaching the group stage after wins over FC DAC 1904 Dunajska Streda, PFC Sochi and C.D.