In 2012, Khasanov was appointed as head coach of Pakhtakors farm club, Pakhtakor-2 Chilanzar.

On 24 July 2012, Numon Khasanov resigned his position and was appointed as head coach of Pakhtakor Youth team.

[3] In January 2014 he was appointed as assistant coach to Samvel Babayan who was named as new trainer of Pakhtakor.

On 7 July 2015, he was named as head coach of Pakhtakor after Samvel Babayan resigned his post to take charge of Uzbek national team.

[4] On 1 May 2023, Khasanov was appointed as Head Coach of Tajikistan Higher League club Khujand.