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The club was formed 1964 under the name Spartak. In 1969 the club was renamed Andijanez. After 1990 the club played in Uzbek League as Navruz Andijan. Since 1997 the club has played as FK Andijan. In 1964–70, 1973–74 and 1986–91 the club played in Soviet League championships.
On 22 August 2012 club hired Azamat Abduraimov as head coach to help Andijan remain in the top division, however the club was relegated to the Uzbekistan First League. The club finished as 2013 season runners-up after Mash'al Mubarek and gained promotion to Uzbek League after a single year in the First League. After the first half of the 2013 season, Andijon was 14th in the league with only 4 points. On 14 June 2014 Andijan lost an away match against Bunyodkor by 1–2. Some days later, on 20 June 2014 Azamat Abduraimov resigned. Orif Mamatkazin, as the interim of the club, was appointed as caretaker. On 26 September 2014 Edgar Gess was appointed as the club's new head coach.
Viktor Kumykov
