2008–09 UEFA Cup knockout stage

The knockout stage of the 2008–09 UEFA Cup began on 18 February 2009, and concluded with the final at the Şükrü Saracoğlu Stadium in Istanbul on 20 May 2009.

The team that had the higher aggregate score over the two legs progressed to the next round.

If away goals are also equal, 30 minutes of extra time were played.

The draw mechanism for each round is as follows: In the final, the tie was played over just one leg at a neutral venue.

If scores were level at the end of normal time in the final, extra time was played, followed by penalties if scores had remained tied.

Of the eight teams who had been placed in Pot 5 of the group stage draw, only Metalist Kharkiv and Saint-Étienne reached the round of 16.

Of the eight teams that entered the Round of the 32 from the UEFA Champions League group stage, two lost: Fiorentina and Bordeaux.

Zenit Saint Petersburg won 4–2 on aggregate.

3–3 on aggregate; Dynamo Kyiv won on away goals.

2–2 on aggregate; Manchester City won 4–3 on penalties.

The final was played on 20 May 2009 at the Şükrü Saracoğlu Stadium in Istanbul, Turkey.