The qualifying rounds for the 2005–06 UEFA Cup began on 14 July 2005. In total, there were two qualifying rounds which narrowed clubs down to 80 teams in preparation for the first round.
First qualifying round
!colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region
First leg
All times CET Match awarded 3-0 to Baskimi due to Žepče fielding an ineligible player ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ----
Second leg
All times CET Bashkimi win 4-1 on aggregate ---- APOEL win 6–0 on aggregate ---- Rapid București win 10–0 on aggregate ---- Široki Brijeg win 4–3 on aggregate ---- 1–1 on aggregate, Vardar won on away goals ---- Omonia won 6–0 on aggregate ---- Domžale won 8–0 on aggregate ---- MTZ-RIPO won 3–2 on aggregate ---- Banants won 4–3 on aggregate ---- BATE Borisov won 6–0 on aggregate ---- Vaduz won 2–1 on aggregate ---- MŠK Žilina won 3–2 on aggregate ---- Mainz 05 won 4–0 on aggregate ---- Nistru Otaci won 5–2 on aggregate ---- Carmarthen Town won 5–3 on aggregate ---- Cork City won 2–1 on aggregate ---- B36 won 3–2 on aggregate ---- Allianssi won 4–1 on aggregate ---- 2–2 on aggregate, Linfield won on away goals ---- Liepājas Metalurgs won 6–0 on aggregate ---- Keflavik won 6–0 on aggregate ---- Viking won 3–1 on aggregate ---- MyPa won 2–1 on aggregate ---- 4–4 on aggregate, Rhyl won on away goals ---- Esbjerg won 7–2 on aggregate
Second qualifying round
!colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region
All times CET Red Star Belgrade win 7–1 on aggregate ---- Maccabi Petah Tikva win 11–0 on aggregate ---- Dinamo București win 4–3 on aggregate ---- 2–2 on aggregate, Lokomotiv Plovdiv win on away goals ---- APOEL win 3–2 on aggregate ---- 2–2 on aggregate, Litex Lovech win on away goals ---- Beşiktaş win 6–1 on aggregate ---- Rapid București win 4–1 on aggregate ---- Levski Sofia win 3–1 on aggregate ---- Široki Brijeg win 5–2 on aggregate ---- 3–3 on aggregate, Domžale win on away goals ---- Krylya Sovetov win 4–0 on aggregate ---- Metalurh Donetsk win 5–1 on aggregate ---- 3–3 on aggregate, Grasshoppers win on away goals ---- Graz win 3–0 on aggregate ---- Austria Wien win 4–3 on aggregate ---- 3–3 on aggregate, Zenit St. Petersburg win on away goals ---- Teplice win 3–2 on aggregate ---- Dyskobolia Grodzisk win 4–1 on aggregate ---- Dnipro Dnipropetrovsk win 8–2 on aggregate ---- Zürich win 5–1 on aggregate ---- Halmstad win 5–3 on aggregate ---- Midtjylland win 4–3 on aggregate ---- Brann win 2–0 on aggregate ---- Genk win 6–2 on aggregate ---- Viking win 3–1 on aggregate ---- 2–2 on aggregate, MyPa win on away goals ---- Copenhagen win 4–0 on aggregate ---- Mainz 05 win 4–0 on aggregate ---- 1–1 on aggregate, Cork City win on away goals ---- 1–1 after extra time, Tromsø win 3–2 on penalties
