The 1988–89 UEFA Cup was the 18th season of the UEFA Cup, the secondary club football competition organised by the Union of European Football Associations (UEFA).

The final was played over two legs at the Stadio San Paolo, Naples, Italy, and at the Neckarstadion, Stuttgart, Germany.

The competition was won by Napoli of Italy, who defeated Stuttgart of Germany by an aggregate result of 5–4 to claim their only major European title.

This was the first final and win in the UEFA Cup by an Italian team since Juventus in 1977, starting a successful era for Italian teams who went on to win six UEFA Cup titles in a seven-year period.

This was the fourth season in which all English clubs were banned from European football competitions A total of 64 teams from 30 UEFA member associations participated in the 1988–89 UEFA Cup, all entering from the first round over six knock-out rounds.

The association ranking based on the UEFA country coefficients is used to determine the number of participating teams for each association: Due to the ongoing English ban, their two births were allocated to associations 10–11, each gaining a third birth.

For the 1988–89 UEFA Cup, the associations are allocated places according to their 1987 UEFA country coefficients, which takes into account their performance in European competitions from 1982–83 to 1986–87.

Matches were scheduled for Wednesdays, except for the first leg of the quarter-finals, which was held on a Tuesday.

RFC Liège won 11–1 on aggregate.

RŠD Velež won 6–2 on aggregate.

Athletic Bilbao won 2–1 on aggregate.

The match was briefly interrupted for an intervention by the fire brigade due to Partizan fans starting a large fire at the stadium's east stand by burning the high jump sponge mat.

Furthermore, Roma captain Giuseppe Giannini got hit in the head with a coin thrown from the stands as Partizan fans pelted the pitch with missiles following one of the Roma goals.

In addition to the SFr200,000 monetary fine, UEFA punished Partizan with a one-match stadium ban, enforced for their 1989–90 Cup Winners' Cup first round tie versus Celtic.

RFC Liège won 3–2 on aggregate.

Victoria București won on away goals.

Bayern Munich won on away goals.