The Azerbaijan Cup 2008–09 was the sixteenth season of the annual cup competition in Azerbaijan. It started on September 17, 2008 with two games of Premiliary Round and ended in May 2009 with the Final held at Tofik Bakhramov Stadium in Baku. Khazar Lenkoran were the defending champions. Eighteen teams compete in this year's competition.
Four lower division teams, qualified for this competition due to unknown reasons, played out two participants who would join the fourteen teams of the Azerbaijan Premier League 2008–09 in the next round. The games were played on September 17 (first legs) and September 24, 2008 (second legs).
The two winners from the Premiliary Round joined fourteen Premier League teams in this round. The first legs were played on October 29 and 30, 2008. The second legs were played on November 5 and 6, 2008.