The final phase of the 1999–2000 UEFA Cup began on 23 November 1999 with the third round and concluded on 17 May 2000 with the final at the Parken Stadium in Copenhagen, Denmark.
[1] A total of 32 teams competed in this phase of the competition.
The following 32 teams qualified for the final phase of the competition.
Deportivo La Coruña won 5–3 on aggregate.
2–2 on aggregate; Borussia Dortmund won 3–1 on penalties.
[7] 2–2 on aggregate; Slavia Prague won on away goals.
The final was played on 17 May 2000 at the Parken Stadium in Copenhagen, Denmark.