Prior to that, Baku played 18 seasons in the Azerbaijan Premier League, winning the championship twice and the National Cup three times.

Led by Shamil Heydarov, Dinamo finished 2nd and entered the 1998–99 UEFA Cup, but was eliminated by Argeş Piteşti 1–7 on aggregate in the preliminary round.

FC Baku gained some important victories over the opponents and was holding a pole position until February 2005.

At the end of the season Asgar Abdullayev concentrated on the Azerbaijan Cup, where his team reached the final.

[7][8] In 2008, Baku appointed Gjoko Hadžievski as their manager, and after a poor first season, the club celebrated their second title.

[10] In 2010, the club was handed a two-match suspension by UEFA for fielding Joël Epalle in the first leg of the second qualifying round of the Europa League against FK Budućnost, who was ineligible to play at the time.

Despite the appointment of famous names such as Bülent Korkmaz, Winfried Schäfer, Aleksandrs Starkovs, Božidar Bandović and Milinko Pantić, the club did not achieve any success and squandered large sums of money on unsuccessful signings.

[16] The club's logo is based on The Maiden Tower, a noted landmark and one of Azerbaijan's most distinctive emblems.