UEFA Europa League
| Season | 1st Leg | 2nd Leg | Aggregate | |
| 1968/69 | Aris Salonica (GRE) vs Hibernians | 1-0 | 6-0 | (7-0) |
| 1969/70 | Dinamo Bacau (ROM) vs Floriana | 6-0 | 1-0 | (7-0) |
| 1970/71 | AB Copenhagen (DEN) vs Sliema W. | 7-0 | 3-2 | (10-2) |
| 1971/72 | Marsa vs Juventus (ITA) | 0-6 | 0-5 | (0-11) |
| 1972/73 | Inter (ITA) vs Valletta | 6-1 | 1-0 | (7-1) |
| 1973/74 | Sliema W. vs Lokomotiv Plovdiv (BUL) | 0-2 | 0-1 | (0-3) |
| 1974/75 | FC Amsterdam (HOL) vs Hibernians | 7-0 | 5-0 * | (12-0) |
| 1975/76 | Sliema W. vs Sporting Lisboa (POR) | 1-2 | 1-3 | (2-5) |
| 1976/77 | Grasshoppers (SWI) vs Hibernians | 7-0 | 2-0 | (9-0) |
| 1977/78 | Eintracht Frankfurt (GER) vs Sliema W. | 5-0 | 0-0 | (5-0) |
| 1978/79 | Sporting Braga (POR) vs Hibernians | 5-0 | 2-3 | (7-3) |
| 1979/80 | Valletta vs Leeds United (ENG) | 0-4 | 0-3 | (0-7) |
| 1980/81 | Sliema W. vs Barcelona (SPA) | 0-2 | 0-1 | (0-3) |
| 1981/82 | Aris Salonica (GRE) vs Sliema W. | 4-0 | 4-2 | (8-2) |
| 1982/83 | Zurrieq vs Hajduk Split (YUG) | 1-4 | 0-4 | (1-8) |
| 1983/84 | Rabat A. vs Inter Bratislava (CZE) | 0-10 | 0-6 | (0-16) |
| 1984/85 | Rabat A. vs Partizan Beograd (YUG) | 0-2 | 0-2 | (0-4) |
| 1985/86 | Hamrun S. vs Dinamo Tirana (ALB) | 0-1 | 0-0 | (0-1) |
| 1986/87 | Hibernians vs Trakia Plovdiv (BUL) | 0-2 | 0-8 | (0-10) |
| 1987/88 | Valletta vs Juventus (ITA) | 0-4 | 0-3 | (0-7) |
| 1988/89 | Sliema W. vs Victoria Bucharest (ROM) | 0-2 | 1-6 | (1-8) |
| 1989/90 | Valletta vs First Wien (AUT) | 1-4 | 0-3 | (1-7) |
| 1990/91 | Hibernians vs Partizan Beograd (YUG) | 0-3 | 0-2 | (0-5) |
| 1991/92 | Neuchatel Xamax (SWI) vs Floriana | 2-0 | 0-0 | (2-0) |
| 1992/93 | Floriana vs Borussia Dortmund (GER) | 0-1 | 2-7 | (2-8) |
| 1993/94 | Trabzonspor (TUR) vs Valletta | 3-1 | 3-1 | (6-2) |
| 1994/95 | Dinamo Minsk (BLR) vs Hibernians | 3-1 | 3-4 aet | (6-5) |
| Valletta vs Rapid Bucharest (ROM) | 2-6 | 1-1 | (3-7) | |
| 1995/96 | Hibernians vs Chernomorets (UKR) | 2-5 | 0-2 | (2-7) |
| Omonoia Nicosia (CYP) vs Sliema W. | 3-0 | 2-1 | (5-1) | |
| 1996/97 | SLIEMA W. vs Margveti Zestaphoni (GEO) | 1-3 | 3-0 | (4-3) |
| Sliema W. vs Odense (DEN) | 0-2 | 1-7 | (1-9) | |
| Beitar Jerusalem (ISR) vs Floriana | 3-1 | 5-1 | (8-2) | |
| 1997/98 | Birkirkara vs Spartak Trnava (SVK) | 0-1 | 1-3 | (1-4) |
| 1998/99 | Shakthar Donetsk (UKR) vs Birkirkara | 2-1 | 4-0 | (6-1) |
| 1999/2000 | Lyngby (DEN) vs Birkirkara | 7-0 | 0-0 | (7-0) |
| Sliema W. vs FC Zurich (SWI) | 0-3 | 0-1 | (0-4) | |
| 2000/01 | NK Rijeka (CRO) vs Valletta FC | 3-2 | 5-4 aet | (8-6) |
| Sliema W. vs Partizan Beograd (YUG) | 2-1 | 1-4 | (3-5) | |
| 2001/02 | SK Matador Puchov (SVK) vs Sliema W. | 3-0 | 1-2 | (4-2) |
| BIRKIRKARA vs Lokomotiv Tbilisi (GEO) | 0-0 | 1-1 | (1-1) ** | |
| Dynamo Moscow (RUS) vs Birkirkara | 1-0 | 0-0 | (1-0) | |
| 2002/03 | Sliema Wanderers vs KS Polonia Warszawa (POL) | 1-3 | 0-2 | 1-5 |
| FC Metalurh Zaporizhya (UKR) vs Birkirkara | 3-0 | 0-0 | 3-0 | |
| 2003/04 | Valletta vs Neuchatel Xamax (SWI) | 0-2 | 0-2 | (0-4) |
| Birkirkara vs Ferencvaros (HUN) | 0-5 | 0-1 | (0-6) | |
| 2004/05 | Marsaxlokk vs NK Primorje (SLO) | 0-1 | 0-2 | (0-3) |
| FK Partizani Tirana (ALB) vs Birkirkara | 4-2 | 1-2 | (5-4) | |
| 2005/06 | Birkirkara vs APOEL FC (CYP) | 0-2 | 0-4 | (0-6) |
| AC Omonia Nicosia (CYP) vs Hibernians | 3-0 | 3-0 | (6-0) | |
| 2006/07 | Rapid Bucharest (ROM) vs Sliema Wanderers | 5-0 | 1-0 | (6-0) |
| Hibernians vs Dinamo Bucharest (ROM) | 0-4 | 1-5 | (1-9) | |
| 2007/08 | Sliema Wanderers vs PFC Litex Lovech (BUL) | 0-3 | 0-4 | (0-7) |
| FK Vojvodina (SRB) vs Hibernians | 5-1 | 2-0 | (7-1) | |
| 2008/09 | HNK Hajduk Split (CRO) vs Birkirkara FC | 4-0 | 3-0 | (7-0) |
| Marsaxlokk FC vs NK Slaven Koprivnica (CRO) | 0-4 | 0-4 | (0-8) | |
| 2009/10 | NK Slaven Koprivnica (CRO) vs Birkirkara FC | 1-0 | 0-0 | (1-0) |
| VALLETTA FC vs Keflavik (ICE) | 3-0 | 2-2 | (5-2) | |
| St. Patrick’s Athletic (IRE) vs Valletta FC | 1-1 | 1-0 | (2-1) | |
| Sliema Wanderers vs Maccabi Netanya (ISR) | 0-0 | 0-3 | (0-3) | |
| 2010/11 | HNK Sibenik (CRO) vs Sliema Wanderers | 0-0 | 3-0 | (3-0) |
| Valletta vs Ruch Chorzow (POL) | 1-1 | 0-0 | (1-1) *** | |
| 2011/12 | Birkirkara vs FK Vllaznia Shkoder | 0-1 | 1-1 | (1-2) |
| Floriana vs AEK Larnaca (CYP) | 0-8 | 0-1 | (0-9) | |
| 2012/13 | Birkirkara vs Metalurg Skopje (MKD) | 2-2 | 0-0 | (2-2) **** |
| IF Elfsborg (SWE) vs Floriana | 8-0 | 4-0 | (12-0) | |
| FK Sarajevo (BOS) vs Hibernians | 5-2 | 4-4 | (9-6) |
* both matches were played in Holland
** Birkirkara qualify on the away-goals rule
*** Ruch Chorzow qualify on the away-goals rule
**** Metalurg Skopje qualify on the away-goals rule
Notes:-
- Names of local clubs in uppercase indicate that the club moved to the next round.
- In seasons 1994-95, 1995-96 and 1996-97, two Maltese clubs participated because clubs coming from small nations were excluded from the Champions Cup.
- As from 1999-2000, two clubs participate in the UEFA Cup, since the Cup Winners Cup will no longer be played.
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