Kupa e shqipërisë 2008–09 was the fifty-seventh season of Albania's annual cup competition. It began on September 24, 2008 with the First Preliminary Round and ended on May 6, 2009 with the Final. The winners of the competition qualified for the second qualifying round of the UEFA Europa League. Vllaznia were the defending champions.
The rounds were played in a two-legged format similar to those of European competitions. If the aggregated score was tied after both games, the team with the higher number of away goals advanced. If the number of away goals was equal in both games, the match was decided by extra time and a penalty shootout, if necessary.
In order to reduce the number of participating teams for the First Round to 32, a preliminary tournament was played. Only teams from the Second Division (III) were allowed to enter. Each Second Division group played its own tournament. In contrast to the main tournament, the preliminary tournament was held as a single-leg knock-out competition.
1Dinamo Tirana were excluded from the Cup because they fielded Elis Bakaj although he previously played in the Cup for Partizani Tirana. Second leg's 0–0 score was annulled and Vllaznia were awarded a 2–0 win.