| Season | Round | 1st Leg | 2nd Leg | Aggregate | |
| 1961/62 | Q | Servette Geneva (SWI) vs Hibernians | 5-0 | 2-1 | (7-1) |
| 1962/63 | R1 | Floriana vs Ipswich Town (ENG) | 1-4 | 0-10 | (1-14) |
| 1963/64 | R1 | Dukla Prague (CZE) vs Valletta | 6-0 | 2-0 | (8-0) |
| 1964/65 | R1 | Sliema Wanderers vs Dinamo Bucharest (ROM) | 0-2 | 0-5 | (0-7) |
| 1965/66 | R1 | Panathinaikos (GRE) vs Sliema Wanderers | 4-1 | 0-1 | (4-2) |
| 1966/67 | Q | Sliema Wanderers vs CSKA Sofia (BUL) | 1-2 | 0-4 | (1-6) |
| 1967/68 | R1 | Manchester United (ENG) vs Hibernians | 4-0 | 0-0 | (4-0) |
| 1968/69 | R1 | Floriana vs Lahden Reipas (FIN) | 1-1 | 0-2 | (1-3) |
| 1969/70 | R1 | Hibernians vs Spartak Trnava (CZE) | 2-2 | 0-4 | (2-6) |
| 1970/71 | R1 | Sporting Lisboa (POR) vs Floriana | 5-0 | 4-0 | (9-0) |
| 1971/72 | R1 | IA Akranes (ICE) vs SLIEMA WANDERERS | 0-4 | 0-0 | (0-4) |
| R2 | Celtic Glasgow (SCO) vs Sliema Wanderers | 5-0 | 2-1 | (7-1) | |
| 1972/73 | R1 | Sliema Wanderers vs Gornik Zabzre (POL) | 0-5 | 0-5 | (0-10) |
| 1973/74 | R1 | Floriana vs Club Bruges (BEL) | 0-8 | 0-2 | (0-10) |
| 1974/75 | R1 | Valletta vs HJK Helsinki (FIN) | 1-0 | 1-4 | (2-4) |
| 1975/76 | R1 | Floriana vs Hajduk Split (YUG) | 0-5 | 0-3 | (0-8) |
| 1976/77 | R1 | Sliema Wanderers vs Turun Palloseura (FIN) | 2-1 | 0-1 | (2-2) [1] |
| 1977/78 | R1 | Floriana vs Panathinaikos (GRE) | 1-1 | 0-4 | (1-5) |
| 1978/79 | R1 | Grasshoppers (SWI) vs Valletta | 8-0 | 5-3 | (13-3) |
| 1979/80 | R1 | Dundalk (EIR) vs Hibernians | 2-0 | 0-1 | (2-1) |
| 1980/81 | Q | Honved (HUN) vs Valletta | 8-0 | 3-0 | (11-0) |
| 1981/82 | R1 | Hibernians vs Red Star Belgrade (YUG) | 1-2 | 1-8 | (2-10) |
| 1982/83 | R1 | Hibernians vs Widzew Lodz (POL) | 1-4 | 1-3 | (2-7) |
| 1983/84 | R1 | Hamrun Spartans vs Dundee United (SCO) | 0-3 | 0-3 | (0-6) |
| 1984/85 | R1 | FK Austria Memphis (AUT) vs Valletta | 4-0 | 4-0 | (8-0) |
| 1985/86 | R1 | Rabat Ajax vs Omonia Nicosia (CYP) | 0-5 | 0-5 | (0-10) |
| 1986/87 | R1 | FC Porto (POR) vs Rabat Ajax | 9-0 | 1-0 | (10-0) |
| 1987/88 | R1 | Rapid Wien (AUT) vs Hamrun Spartans | 6-0 | 1-0 | (7-0) |
| 1988/89 | R1 | Hamrun Spartans vs Nentori Tirana (ALB) | 2-1 | 0-2 | (2-3) |
| 1989/90 | R1 | Sliema Wanderers vs Nentori Tirana (ALB) | 1-0 | 0-5 | (1-5) |
| 1990/91 | R1 | Valletta vs Rangers Glasgow (SCO) | 0-4 | 0-6 | (0-10) |
| 1991/92 | R1 | Hamrun Spartans vs Benfica (POR) | 0-6 | 0-4 | (0-10) |
| 1992/93 | Q | Valletta vs Maccabi Tel Aviv (ISR) | 1-2 | 0-1 | (1-3) |
| 1993/94 | Q | Ekranas (LIT) vs FLORIANA | 0-1 | 0-1 | (0-2) |
| R1 | Porto (POR) vs Floriana | 2-0 | 0-0 | (2-0) | |
| 1997/98 | Q1 | Valletta vs Skonto Riga (LAT) | 1-0 | 0-2 | (1-2) |
| 1998/99 | Q1 | Valletta vs Anorthosis Famagusta (CYP) | 0-2 | 0-6 | (0-8) |
| 1999/2000 | Q1 | Barry Town (WAL) vs VALLETTA | 0-0 | 2-3 | (2-3) |
| Q2 | SK Rapid Wien vs Valletta | 3-0 | 2-0 | (5-0) | |
| 2000/01 | Q1 | Birkirkara vs KR Reykjavík (ICE) | 1-2 | 1-4 | (2-6) |
| 2001/02 | Q1 | Valletta vs FC Haka Valkeakoski (FIN) | 0-0 | 0-5 | (0-5) |
| 2002/03 | Q1 | HIBERNIANS vs Shelbourne FC (IRE) | 2-2 | 1-0 | (3-2) |
| Q2 | Boavista FC vs Hibernians | 4-0 | 3-3 | (7-3) | |
| 2003/04 | Q1 | SLIEMA WANDERERS vs Skonto Riga (LAT) | 2-0 | 1-3 | (3-3) [2] |
| Q2 | FC Copenhagen (DEN) vs Sliema Wanderers | 4-1 | 6-0 | (10-1) | |
| 2004/05 | Q1 | Sliema Wanderers vs FBK Kaunas (LIT) | 0-2 | 1-4 | (1-6) |
| 2005/06 | Q1 | Sliema Wanderers vs FC Sheriff Tiraspol (MOL) | 1-4 | 0-2 | (1-6) |
| 2006/07 | Q1 | Birkirkara vs B36 Torshavn (FAR) | 0-3 | 2-2 | (2-5) |
| 2007/08 | Q1 | Marsaxlokk vs FK Sarajevo (BOS) | 0-6 | 1-3 | (1-9) |
| 2008/09 | Q1 | Valletta FC vs FC Artmedia Petržalka (SVK) | 0-2 | 0-1 | (0-3) |
| 2009/10 | Q1 | Hibernians vs FK Mogren (MNE) | 0-2 | 0-4 | (0-6) |
| 2010/11 | Q1 | Santa Coloma (AND) vs BIRKIRKARA | 0-3 [3] | 3-4 | (3-7) |
| Q2 | Birkirkara vs MSK Zilina (SVK) | 1-0 | 0-3 | (1-3) | |
| 2011/12 | Q1 | SP Tre Fiori (SMR) vs VALLETTA | 0-3 | 1-2 | (1-5) |
| Q2 | Valletta vs FK Ekranas (LIT) | 2-3 | 0-1 | (2-4) | |
| 2012/13 | Q1 | VALLETTA vs FC Lusitans (AND) | 8-0 | 1-0 | (9-0) |
| Q2 | Valletta vs FK Partizan Belgrade (SRB) | 1-4 | 1-3 | (2-7) | |
| 2013/14 | Q2 | Birkirkara vs NK Maribor (SLO) | 0-0 | 0-2 | (0-2) |
| 2014/15 | Q2 | Valletta vs Qarabagh FK (AZE) | 0-1 | 0-4 | (0-5) |
| 2015/16 | Q2 | Hibernians vs Maccabi Tel Aviv (ISR) | 2-1 | 1-5 | (3-6) |
| 2016/17 | Q1 | VALLETTA vs B36 Tórshavn (FAR) | 1-0 | 1-2 | (2-2) [4] |
| Q2 | Valletta vs FK Crvena zvezda (SRB) | 1-2 | 1-2 | (2-4) | |
| 2017/18 | Q1 | HIBERNIANS vs FCI Tallinn (EST) | 2-0 | 1-0 | (3-0) |
| Q2 | Hibernians vs FC (Red Bull) Salzburg (AUT) | 0-3 | 0-3 | (0-6) | |
| 2018/19 | Q1 | FK Kukesi (ALB) vs Valletta | 0-0 | 1-1 | (1-1) [5] |
| 2019/20 | Q1 | F91 Dudelange (LUX) vs VALLETTA | 2-2 | 1-1 | (3-3) [6] |
| Q2 | Ferencvarosi TC (HUN) vs Valletta | 3-1 | 1-1 | 4-2 | |
| 2020/21 | Q1 | Floriana vs CFR Cluj (ROM) | 0-2 | [7] | |
| 2021/22 | Q1 | FC Flora Tallinn (EST) vs Hibernians | 2-0 | 3-0 | (5-0) |
| 2022/23 | Q1 | Shamrock Rovers (IRE) vs Hibernians | 3-0 | 0-0 | (3-0) |
| 2023/24 | Q1 | Hamrun Spartans vs Maccabi Haifa (ISR) | 0-4 | 1-2 | (1-6) |
| 2024/25 | Q1 | Hamrun Spartans vs Lincoln Red Imps (GIB) | 0-1 | 1-0 aet | (1-1)(4-5 pen) |
[1] Turun Palloseura qualify on the away goal.
[2] Sliema Wanderers qualify on the away goal.
[3] Birkirkara were awarded a walk-over (3-0) in the first leg.
[4] Valletta qualify on the away-goals rule
[5] Kukesi qualify on the away-goals rule
[6] Valletta qualify on the away-goals rule
[7] Played in a single leg
Notes:-
- Names of local clubs in uppercase indicate that the club moved to the next round.
- Between seasons 1994-95 and 1996-97, no Maltese club participated in this competition because with the introduction of the Champions League, clubs coming from small nations were excluded. However they were re-instated in season 1997-98
- As from 2021/22, the away-goals rule has been abolished.