The 2008–09 Swiss Cup was the 84th season of Switzerland's annual cup competition. It began on 20 September with the first games of Round 1 and ended on 20 May 2009 with the Final held at Stade de Suisse, Bern. The winners earned a place in the play-off round of the UEFA Europa League. FC Basel were the defending champions.

Participating clubs

Nine Super League teams (FC Vaduz are from Liechtenstein and thus play in the 2008–09 Liechtenstein Cup) and all sixteen Challenge League clubs entered this year's competition, as well as thirteen teams from 1. Liga and 26 teams from lower leagues (their level within the Swiss league pyramid is given in parentheses below). Teams from 1. Liga and below had to qualify through separate qualifying rounds within their leagues.

Round 1

Teams from Super League and Challenge League were seeded in this round. In a match, the home advantage was granted to the team from the lower league, if applicable.

Round 2

The winners of Round 1 played in this round. Teams from Super League were seeded. In a match, the home advantage was granted to the team from the lower league, if applicable.

Round 3

The winners of Round 2 played in this round. In a match, the home advantage was granted to the team from the lower league, if applicable. Some games were postponed due to snow, and subsequently played elsewhere.

Quarter-finals

The winners of Round 3 played in this round.

Semi-finals

The winners of the quarter-finals played in this round. As in the previous round, matches were openly drawn, meaning that the team drawn first in a match earned the home game.

Final