The 1998 UEFA Intertoto Cup finals were won by Valencia, Werder Bremen, and Bologna.

The 1998 tournament saw Spanish clubs debut in the competition and also the return of English clubs, since the controversy surrounding its participants in 1995.

Match awarded because Leiftur fielded an ineligible player.

TPS won on away goals rule.

Inkaras Kaunas 1–1 Baki Fahlasi on aggregate.

Akademisk Boldklub 3–3 Vorskla Poltava on aggregate.

Vorskla Poltava won on away goals rule.

Lommel won on away goals rule.

Espanyol won on away goals rule.

Ruch Chorzów won on away goals rule.

Debrecen won on away goals rule.

Ruch Chorzów 2–2 Estrela da Amadora on aggregate.

Ruch Chorzów won 4–2 on penalties.

Bologna won on away goals rule.