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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.
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.