[3] In 2002 after first season half Khaydarov was acting head coach of Pakhtakor, replacing Tachmurad Agamuradov.

On 25 July 2005, Khaydarov left his temporary position of trainer and replaced by Bobby Houghton[4] In October 2008, Khaydarov resigned his position of Pakhtakor head coach, after his club lost Metallurg Bekabad with 1:2, widening gap between Kuruvchi.

[9] On 24 June 2014 UFF appointed Khaydarov as new head coach of Uzbekistan U-19 to prepare team for 2014 AFC U-19 Championship in Myanmar.

On 30 April 2017 Khaydarov was appointed as new head coach of Uzbekistan U-22 to prepare team for upcoming qualification matches of 2018 AFC U-23 Championship in China.

His success named him as candidate for manager of senior side, which is preparing for the 2019 AFC Asian Cup.