He started managing career at sport internat of Turkmenistan Sport Committee in 1982, until 1990. After that he trained
Nebitchi Balkanabat from 1990 to 1993. He was coach of
Turkmenistan in football tournament of
1994 Asian Games in
Hiroshima. In 2001–2005 he was head coach of
Pakhtakor Tashkent and 2004 was named as
Coach of the Year. On September 28, 2011, after
Ravshan Khaydarov was sacked and Murod Ismailov replaced him as temporary caretaker of the club, Agamuradov became assistant coach to Ismailov, returning to the club. In June 2012 Agamuradov was appointed as head coach of
FK Buxoro, replacing Jamshid Saidov. On 10 November 2013 he left his position in
FK Buxoro. In 2014, he was named as trainer of
Dinamo Samarqand. On 2 July 2015 he announced that he is resigning his post at
Dinamo. After leaving
Dinamo, on 10 July 2015 he started working as consultant coach at
FK Buxoro. ==Managerial honours==