Draw
2025/261/8-finals
| 1 | Hamrun | Bye | |
| 4 | Bye | Maccabi Tel Aviv | |
| 24 | Bye | Young Boys | |
| 32 | Bye | Sigma Olomouc | |
| 33 | Panathinaikos | Bye | |
| 35 | Besiktas | Bye | |
| 36 | Shakhtar Donetsk | Ilves | 0 : 0, 6 : 0 |
| 40 | Bye | Samsunspor | |
| 41 | Aberdeen | Bye | |
| 45 | FCSB | Bye | |
| 48 | Bye | Drita | |
| 56 | Bye | Genk | |
| 57 | Fredrikstad | Bye | |
| 59 | Midtjylland | Bye | |
| 60 | Bye | Hibernian | |
| 61 | RFS | Bye | |
| 64 | Bye | KuPS | |
| 65 | Lincoln Red Imps | Bye | |
| 68 | Bye | Noah | |
| 69 | Lugano | Bye | |
| 70 | Paks | CFR Cluj | 0 : 3, 0 : 0 |
| 71 | Levski Sofia | H. Beer Sheva | 2 : 1, 0 : 0 |
| 72 | Bye | Braga | |
| 73 | Zrinjski | Bye | |
| 76 | Bye | Breidablik | |
| 77 | Servette | Bye | |
| 79 | Sheriff Tiraspol | Prishtina | 1 : 2, 4 : 0 |
| 80 | Bye | Utrecht | |
| 81 | Anderlecht | Bye | |
| 82 | Trnava | Hacken | 2 : 2, 0 : 1 |
| 84 | Bye | Brann | |
| 85 | Sabah Baku | Celje | 3 : 3, 2 : 3 |
| 86 | AEK Larnaca | Partizan | 2 : 2, 1 : 0 |
| 87 | Ostrava | Bye | |
| 88 | Legia | Aktobe | 1 : 0, 1 : 0 |
| 89 | Rijeka | Bye | |
| 92 | Bye | Shelbourne | |
| 93 | PAOK | Bye | |
| 96 | Bye | Wolfsberger AC |
Quarter-finals
| 1 | Hamrun | Bye | |
| 2 | Bye | Maccabi Tel Aviv | |
| 12 | Bye | Young Boys | |
| 16 | Bye | Sigma Olomouc | |
| 17 | Panathinaikos | Bye | |
| 18 | Besiktas | Shakhtar Donetsk | 0 : 2, 2 : 4 |
| 20 | Bye | Samsunspor | |
| 21 | Aberdeen | Bye | |
| 23 | FCSB | Bye | |
| 24 | Bye | Drita | |
| 28 | Bye | Genk | |
| 29 | Fredrikstad | Bye | |
| 30 | Midtjylland | Hibernian | 2 : 1, 1 : 1 |
| 31 | RFS | Bye | |
| 32 | Bye | KuPS | |
| 33 | Lincoln Red Imps | Bye | |
| 34 | Bye | Noah | |
| 35 | Lugano | CFR Cluj | 0 : 1, 0 : 0 |
| 36 | Levski Sofia | Braga | 0 : 1, 0 : 0 |
| 37 | Zrinjski | Bye | |
| 38 | Bye | Breidablik | |
| 39 | Servette | Bye | |
| 40 | Sheriff Tiraspol | Utrecht | 1 : 4, 1 : 3 |
| 41 | Anderlecht | Hacken | 1 : 3, 1 : 0 |
| 42 | Bye | Brann | |
| 43 | Celje | AEK Larnaca | 1 : 2, 1 : 1 |
| 44 | Ostrava | Legia | 1 : 2, 2 : 2 |
| 45 | Rijeka | Bye | |
| 46 | Bye | Shelbourne | |
| 47 | PAOK | Bye | |
| 48 | Bye | Wolfsberger AC |
Semi-finals
| 1 | Hamrun | Maccabi Tel Aviv | 1 : 2 |
| 6 | Bye | Young Boys | |
| 8 | Bye | Sigma Olomouc | |
| 9 | Panathinaikos | Shakhtar Donetsk | 0 : 0 |
| 10 | Bye | Samsunspor | |
| 11 | Aberdeen | Bye | |
| 12 | FCSB | Drita | 3 : 2 |
| 14 | Bye | Genk | |
| 15 | Fredrikstad | Midtjylland | 1 : 3 |
| 16 | RFS | KuPS | 1 : 2 |
| 17 | Lincoln Red Imps | Noah | 1 : 1 |
| 18 | CFR Cluj | Braga | 1 : 2 |
| 19 | Zrinjski | Breidablik | 1 : 1 |
| 20 | Servette | Utrecht | 1 : 3 |
| 21 | Hacken | Brann | 0 : 2 |
| 22 | AEK Larnaca | Legia | 4 : 1 |
| 23 | Rijeka | Shelbourne | 1 : 2 |
| 24 | PAOK | Wolfsberger AC | 0 : 0 |
Final
| 1 | TBD #1 | Bye | |
| 3 | Bye | Young Boys | |
| 4 | Bye | Sigma Olomouc | |
| 5 | TBD #9 | Samsunspor | |
| 6 | Aberdeen | TBD #12 | |
| 7 | Bye | Genk | |
| 8 | TBD #15 | TBD #16 | |
| 9 | TBD #17 | TBD #18 | |
| 10 | TBD #19 | TBD #20 | |
| 11 | TBD #21 | TBD #22 | |
| 12 | TBD #23 | TBD #24 |
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