The qualifying rounds for the 2008–09 UEFA Cup began on 17 July 2008. In total, there were two qualifying rounds which narrowed clubs down to 80 teams in preparation for the first round.
|-!colspan="5"|Southern-Mediterranean region|-!colspan="5"|Central-East region|-!colspan="5"|Northern region|}
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Nordsjælland win 8–0 on aggregate----Manchester City win 4–0 on aggregate----St Patrick's Athletic win 3–0 on aggregate----2–2 on aggregate, Djurgården win on away goals----Sūduva win 2–0 on aggregate----København win 11–0 on aggregate----Haka win 6–2 on aggregate----Midtjylland win 10–1 on aggregate----Cherno More win 9–0 on aggregate----APOEL win 1–0 on aggregate----Zrinjski Mostar win 5–1 on aggregate----Široki Brijeg win 3–1 on aggregate----Ironi Kiryat Shmona win 4–1 on aggregate----Vllaznia Shkodër win 2–1 on aggregate----Ljubljana win 2–1 on aggregate----Hapoel Tel Aviv win 5–0 on aggregate----Hajduk Split win 7–0 on aggregate----Omonia win 4–1 on aggregate----Slaven Belupo win 8–0 on aggregate----Salzburg win 10–0 on aggregate----Győr win 3–2 on aggregate----Bellinzona win 4–1 on aggregate----Borac Čačak win 4–2 on aggregate----Austria Wien win 2–1 on aggregate----Hertha BSC win 8–1 on aggregate----Lech Poznań win 5–1 on aggregate----Legia Warszawa win 4–1 on aggregate----WIT win 3–2 on aggregate----MŠK Žilina win 3–2 on aggregate----Debrecen win 2–1 on aggregate----Vojvodina win 2–1 on aggregate----FH win 8–3 on aggregate----Viking win 2–1 on aggregate----Kalmar win 10–1 on aggregate----Honka win 4–2 on aggregate----Liepājas Metalurgs win 3–1 on aggregate----Brøndby win 3–0 on aggregate
|-!colspan="5"|Southern-Mediterranean region|-!colspan="5"|Central-East region|-!colspan="5"|Northern region|}
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Match played as a one off in Austria due to political unrest in Georgia
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Borac Čačak win 2–1 on aggregate----
Nordsjælland win 4–2 on aggregate----
Kalmar win 5–2 on aggregate----
1–1 on aggregate, Manchester City win 4–2 on penalties----
Honka win 2–1 on aggregate----
Brøndby win 6–0 on aggregate----
Rennes win 3–2 on aggregate----
Copenhagen win 7–3 on aggregate----
St Patrick's win 4–3 on aggregate----
Aston Villa win 5–2 on aggregate----
Beşiktaş win 6–1 on aggregate----
Braga win 3–0 on aggregate----
Hapoel Tel Aviv win 3–0 on aggregate----Slaven Belupo win 2–1 on aggregate----Litex Lovech win 2–1 on aggregate----Deportivo win 2–0 on aggregate----APOEL 5–5 Red Star Belgrade on aggregate, APOEL win on away goals----Napoli win 8–0 on aggregate----Cherno More win 3–1 on aggregate----Omonia win 3–2 on aggregate----Vaslui win 5–1 on aggregate----Zürich 2–2 Sturm Graz on aggregate. Zürich won 4–2 on penalties.----Stuttgart win 6–2 on aggregate----Lech Poznań win 6–0 on aggregate----Žilina win 4–2 on aggregate----Match played as a one off in Austria due to political unrest in Georgia.----
Young Boys win 7–3 on aggregate----
FC Moscow win 4–1 on aggregate----
4–4 on aggregate, Bellinzona win on away goals----
Hertha BSC win 3–0 on aggregate----
Salzburg win 4–2 on aggregate----
Rosenborg win 6–2 on aggregate