The club was established in 1954, even though it never participated at any Soviet football league. It was re-established in 1993. Shamkir's most successful years were at the start of the 2000s, after Shahbaz Suleymanov's takeover, club with Agaselim Mirjavadov consecutively won three Azerbaijan Premier League titles and reached the final of Azerbaijan Cup three times. The club also became the first Azerbaijani team to pass qualifying stage of Champions League. In 2005, the club was briefly defunct due to sponsorship reasons but re-established once again on 19 August 2009 after finding sponsors.