The 1988–89 UEFA Cup was won by Napoli over Stuttgart. It was the fourth season that English clubs were banned from European competitions. The English league clubs who otherwise would have qualified were Manchester United and Luton Town. Romania ceded a place to Sweden. German title holders obtained a place for another Albanian retirement.
Stuttgart won 3–2 on aggregate. ---- Bayern München won 10–4 on aggregate. ---- 2–2 on aggregate. Groningen won on away goals. ---- Lokomotive Leipzig won 7–0 on aggregate. ---- Heart of Midlothian won 4–0 on aggregate. ---- Austria Wien won 5–4 on aggregate. ---- Sporting Clube de Portugal won 6–3 on aggregate. ---- 4–4 on aggregate. Real Sociedad won on away goals. ---- RFC Liège won 11–1 on aggregate. ---- Internazionale won 4–2 on aggregate. ---- Újpesti Dózsa won 2–1 on aggregate. ---- Rangers won 5–2 on aggregate. ---- Dynamo Dresden won 2–0 on aggregate. ---- Bordeaux won 3–2 on aggregate. ---- Dunajská Streda won 6–2 on aggregate. ---- 1–1 on aggregate. TPS won on away goals. ---- Waregem won 5–1 on aggregate. ---- Malmö FF won 3–2 on aggregate. ---- 2–2 on aggregate. First Vienna won on away goals. ---- Juventus won 5–1 on aggregate. ---- RŠD Velež won 6–2 on aggregate. ---- Athletic Club won 2–1 on aggregate. ---- Benfica won 6–1 on aggregate. ---- Victoria București won 8–1 on aggregate. ---- Napoli won 2–1 on aggregate. ---- Partizan won 10–0 on aggregate. ---- Servette won 1–0 on aggregate. ---- Dinamo Minsk won 2–1 on aggregate. ---- Dinamo Zagreb won 2–1 on aggregate. ---- Köln won 6–3 on aggregate. ---- Belenenses won 2–0 on aggregate. ---- Roma won 4–3 on aggregate.
Bayern München won 5–1 on aggregate. ---- Köln won 3–1 on aggregate. ---- Stuttgart won 4–2 on aggregate. ---- 4–4 on aggregate. Roma won on away goals. ---- 0–0 on aggregate. RŠD Velež won 4–3 on penalties. ---- Real Sociedad won 2–1 on aggregate. ---- Heart of Midlothian won 1–0 on aggregate. ---- Napoli won 3–1 on aggregate. ---- Bordeaux won 2–0 on aggregate. ---- Juventus won 7–4 on aggregate. ---- Dynamo Dresden won 5–3 on aggregate. ---- 2–2 on aggregate. TPS won on away goals. ---- Internazionale won 2–1 on aggregate. ---- RFC Liège won 3–2 on aggregate. ---- Groningen won 3–1 on aggregate. ---- 2–2 on aggregate. Victoria București won on away goals.
Third round
First leg
---- ---- ---- ---- ---- ---- ----
Second leg
3–3 on aggregate. Bayern München won on away goals. ---- Real Sociedad won 3–2 on aggregate. ---- Stuttgart won 5–1 on aggregate. ---- Heart of Midlothian won 4–2 on aggregate. ---- Napoli won 1–0 on aggregate. ---- Dynamo Dresden won 4–0 on aggregate. ---- Juventus won 2–0 on aggregate. ---- 3–3 on aggregate. Victoria București won on away goals.
Quarter-finals
First leg
---- ---- ----
Second leg
1–1 on aggregate. Stuttgart won 4–2 on penalties. ---- Bayern München won 2–1 on aggregate. ---- Napoli won 3–2 on aggregate. ---- Dynamo Dresden won 5–1 on aggregate.
Semi-finals
First leg
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Second leg
Napoli won 4–2 on aggregate. ---- Stuttgart won 2–1 on aggregate.
