Cupa UEFA 1998-1999 a fost câștigată de Parma în finala cu Marseille. A fost a doua Cupă UEFA câștigată de Parma după cea din sezonul 1994-1995.

A fost ultima ediție care a folosit acest format competițional. Cupa Cupelor UEFA a fost desființată, iar echipele care au câștigat cupeke în țările lor aveau să joace în Cupa UEFA, ceea ce a dus la adăugarea unei noi runde de calificări.

Prima rundă de calificare

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Echipa 1 Scor gen. Echipa 2   Tur     Retur  
FC Argeș Pitești   7-1   Dynamo Baku 5-1 2-0
FC Belshyna Babruisk   1-3   PFC CSKA Sofia 0-0 1-3
AC Omonia   8-6   Linfield F.C. 5-1 3-5
FC Shakhtar Donetsk   6-1   Birkirkara F.C. 2-1 4-0
FC Kolkheti Poti   0-11   Steaua Roșie Belgrad 0-4 0-7
FK Inter Bratislava   4-0   SK Tirana 2-0 2-0
Tallinna Sadam   1-5   Polonia Warszawa 0-2 1-3
HB Tórshavn   2-4   Vaasan Palloseura 2-0 0-4
FK Željezničar   1-2   Kilmarnock F.C. 1-1 0-1
NK Mura Murska Sobota   8-2   Daugava Riga 6-1 2-1
ÍA   3-3(a)   FK Žalgiris Vilnius 3-2 0-1
Hapoel Tel Aviv FC   6-2   FinnPa 3-1 3-1
FC Shirak   0-7   Malmö FF 0-2 0-5
Germinal Ekeren   4-1   FK Sarajevo 4-1 0-0
Shelbourne F.C.   3-7   Rangers F.C. 3-5 0-2
Oțelul Galați   4-1   FK Sloga Jugomagnat 3-0 1-1
Union Luxembourg   0-7   IFK Göteborg 0-3 0-4
Ferencvárosi TC   14-1   Principat 6-0 8-1
Tiligul Tiraspol   0-6   R.S.C. Anderlecht 0-1 0-5
Newtown AFC   0-7   Wisła Kraków 0-0 0-7

A doua rundă de calificare

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Echipa 1 Scor gen. Echipa 2   Tur     Retur  
Steaua Roșie Belgrad   4-2   SC Rotor Volgograd 2-1 2-1
Ferencvárosi TC   4-6   AEK Athena 4-2 0-4
Germinal Ekeren   3-5   Servette FC 1-4 2-1
FC Argeș Pitești   (a)4-4   Istanbulspor AS 2-0 2-4
Molde FK   0-2   PFC CSKA Sofia 0-0 0-2
IFK Göteborg   2-2(a)   Fenerbahçe SK 2-1 0-1
NK Mura Murska Sobota   0-2   Silkeborg IF 0-0 0-2
Rangers F.C.   2-0   PAOK FC 2-0 0-0
SK Slavia Praha   4-2   FK Inter Bratislava 4-0 0-2
FC Zürich   6-3   FC Shakhtar Donetsk 4-0 2-3
S.K. Brann   1-0   FK Žalgiris Vilnius 1-0 0-0
Wisła Kraków   7-2   Trabzonspor 5-1 2-1
Vejle BK   6-0   Oțelul Galați 3-0 3-0
Hapoel Tel Aviv FC   1-1(p)   Strømsgodset I.F. 1-0 0-1(aet)
NK Osijek   3-3(a)   R.S.C. Anderlecht 3-1 0-2
AC Omonia   3-3(a)   SK Rapid Wien 3-1 0-2
Vaasan Palloseura   0-3   Grazer AK 0-0 0-3
Polonia Warszawa   0-2   FC Dynamo Moscow 0-1 0-1
Hajduk Split   3-2   Malmö FF 1-1 2-1
SK Sigma Olomouc   4-0   Kilmarnock F.C. 2-0 2-0

Prima runda

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Echipa 1 Scor gen. Echipa 2   Tur     Retur  
AC Sparta Praha   2-5   Real Sociedad 2-4 0-1
Fenerbahçe SK   2-3   Parma F.C. 1-0 1-3
Blackburn Rovers F.C.   2-3   Olympique Lyonnais 0-1 2-2
FC Dynamo Moscow   5-4   Skonto FC 2-2 3-2
Vitória SC   2-4   Celtic F.C. 1-2 1-2
VfB Stuttgart   4-3   Feyenoord Rotterdam 1-3 3-0
FC Argeș Pitești   0-8   Celta de Vigo 0-1 0-7
Silkeborg IF   0-3   A.S. Roma 0-2 0-1
ŁKS Łódź   1-3   AS Monaco FC 1-3 0-0
PFC Litex Lovech   1-3   Grazer AK 1-1 0-2
R.S.C. Anderlecht   0-2   Grasshopper-Club Zürich 0-0 0-2
ACF Fiorentina   2-1   Hajduk Split 2-1 0-0
Aston Villa F.C.   6-2   Strømsgodset I.F. 3-2 3-0
FC Schalke 04   1-1(p)   SK Slavia Praha 1-0 0-1(aet)
Servette FC   2-2(a)   PFC CSKA Sofia 2-1 0-1
Steaua Roșie Belgrad   (p)3-3   FC Metz 2-1 1-2(aet)
FC Košice   0-8   Liverpool F.C. 0-3 0-5
Sporting Clube de Portugal   1-4   Bologna F.C. 1909 0-2 1-2
NK Maribor   0-5   Wisła Kraków 0-2 0-3
Vejle BK   1-5   Real Betis 1-0 0-5
FC Girondins de Bordeaux   3-2   SK Rapid Wien 1-1 2-1
Atlético Madrid   3-0   FK Obilic 2-0 1-0
Beitar Ierusalim   3-5   Rangers F.C. 1-1 2-4
Leeds United A.F.C.   (p)1-1   CS Marítimo 1-0 0-1(aet)
Udinese Calcio   1-2   Bayer Leverkusen 1-1 0-1
Steaua București   3-7   Valencia CF 3-4 0-3
Willem II Tilburg   6-0   FC Dinamo Tbilisi 3-0 3-0
FC Zürich   7-2   Anorthosis Famagusta FC 4-0 3-2
Újpest FC   2-7   Club Brugge 0-5 2-2
Vitesse Arnhem   6-3   AEK Atena 3-0 3-3
S.K. Brann   2-4   Werder Bremen 2-0 0-4(aet)
SK Sigma Olomouc   2-6   Olympique de Marseille 2-2 0-4

A doua runda

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Echipa 1 Scor gen. Echipa 2   Tur     Retur  
FC Dynamo Moscow   2-6   Real Sociedad 2-3 0-3
PFC CSKA Sofia   2-5   Atlético Madrid 2-4 0-1
A.S. Roma   1-0   Leeds United A.F.C. 1-0 0-0
Celtic F.C.   3-5   FC Zürich 1-1 2-4
Grasshopper-Club Zürich   3-2   ACF Fiorentina 0-2 3-0
Vitesse Arnhem   1-3   FC Girondins de Bordeaux 0-1 1-2
Bayer Leverkusen   2-3   Rangers F.C. 1-2 1-1
Wisła Kraków   2-3   Parma F.C. 1-1 1-2
Grazer AK   3-7   AS Monaco FC 3-3 0-4
Werder Bremen   3-4   Olympique de Marseille 1-1 2-3
Celta de Vigo   3-2   Aston Villa F.C. 0-1 3-1
Liverpool F.C.   (a)2-2   Valencia CF 0-0 2-2
Bologna F.C. 1909   4-1   SK Slavia Praha 2-1 2-0
Willem II Tilburg   1-4   Real Betis 1-1 0-3
Steaua Roșie Belgrad   3-5   Olympique Lyonnais 1-2 2-3
VfB Stuttgart   3-4   Club Brugge 1-1 2-3(aet)
Echipa #1   Total   Echipa #2   Tur     Retur  
Real Sociedad   3-5   Atlético Madrid 2-1 1-4(aet)
A.S. Roma   3-2   FC Zürich 1-0 2-2
Grasshopper-Club Zürich   3-3(a)   FC Girondins de Bordeaux 3-3 0-0
Rangers F.C.   2-4   Parma F.C. 1-1 1-3
AS Monaco FC   2-3   Olympique de Marseille 2-2 0-1
Celta de Vigo   4-1   Liverpool F.C. 3-1 1-0
Bologna F.C. 1909   4-2   Real Betis 4-1 0-1
Olympique Lyonnais   5-3   Club Brugge 1-0 4-3

Sferturi de finala

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Echipa #1   Total   Echipa #2   Tur     Retur  
Atlético Madrid   4-2   A.S. Roma 2-1 2-1
FC Girondins de Bordeaux   2-7   Parma F.C. 2-1 0-6
Olympique de Marseille   2-1   Celta de Vigo 2-1 0-0
Bologna F.C. 1909   3-2   Olympique Lyonnais 3-0 0-2

Semifinale

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Echipa #1   Total   Echipa #2   Tur     Retur  
Atlético Madrid   2-5   Parma F.C. 1-3 1-2
Olympique de Marseille   (a)1-1   Bologna F.C. 1909 0-0 1-1