Draw
2025/261/8-finals
| 1 | Rijeka | Bye | |
| 2 | Ludogorets | Din. Minsk | 2 : 2, 1 : 0 |
| 3 | Noah | Buducnost | 2 : 2, 1 : 0 |
| 4 | Bye | Ferencvaros | |
| 5 | TNS | Shkendija | 1 : 2, 0 : 0 |
| 6 | FCSB | Inter Escaldes | 1 : 2, 3 : 1 |
| 7 | Shelbourne | Linfield | 1 : 1, 1 : 0 |
| 8 | Bye | Qarabag | |
| 9 | Lech Poznan | Bye | |
| 10 | Egnatia | Breidablik | 0 : 5, 1 : 0 |
| 11 | Vikingur | Lincoln Red Imps | 0 : 1, 2 : 3 |
| 12 | Bye | Crvena zvezda | |
| 13 | Zalgiris | Hamrun | 0 : 3, 2 : 0 |
| 14 | Bye | Dyn. Kyiv | |
| 15 | Pafos | Bye | |
| 16 | Bye | Maccabi Tel Aviv | |
| 17 | Bodo/Glimt | Bye | |
| 24 | Bye | Sturm Graz | |
| 25 | Celtic | Bye | |
| 29 | KuPS | Milsami | 0 : 0, 1 : 0 |
| 30 | O. Ljubljana | Kairat Almaty | 0 : 2, 1 : 1 |
| 31 | Slovan Bratislava | Bye | |
| 32 | Virtus | Zrinjski | 1 : 2, 0 : 2 |
| 33 | Basel | Bye | |
| 37 | Levadia | RFS | 0 : 1, 0 : 1 |
| 38 | Iberia 1999 | Malmo FF | 1 : 3, 1 : 3 |
| 39 | FC Copenhagen | Bye | |
| 40 | Drita | Differdange | 3 : 2, 1 : 0 |
| 41 | Feyenoord | Bye | |
| 44 | Bye | Fenerbahce | |
| 45 | Nice | Bye | |
| 48 | Bye | Benfica | |
| 49 | Rangers | Bye | |
| 50 | Bye | Panathinaikos | |
| 51 | Plzen | Bye | |
| 52 | Bye | Servette | |
| 53 | Brann | Bye | |
| 54 | Bye | Salzburg | |
| 56 | Bye | Club Brugge KV |
Quarter-finals
| 1 | Rijeka | Ludogorets | 1 : 3, 0 : 0 |
| 2 | Noah | Ferencvaros | 3 : 4, 1 : 2 |
| 3 | Shkendija | FCSB | 2 : 1, 1 : 0 |
| 4 | Shelbourne | Qarabag | 0 : 1, 0 : 3 |
| 5 | Lech Poznan | Breidablik | 1 : 0, 7 : 1 |
| 6 | Lincoln Red Imps | Crvena zvezda | 1 : 5, 0 : 1 |
| 7 | Hamrun | Dyn. Kyiv | 0 : 3, 0 : 3 |
| 8 | Pafos | Maccabi Tel Aviv | 1 : 0, 1 : 1 |
| 9 | Bodo/Glimt | Bye | |
| 12 | Bye | Sturm Graz | |
| 13 | Celtic | Bye | |
| 15 | KuPS | Kairat Almaty | 0 : 3, 2 : 0 |
| 16 | Slovan Bratislava | Zrinjski | 2 : 2, 4 : 0 |
| 17 | Basel | Bye | |
| 19 | RFS | Malmo FF | 0 : 1, 1 : 4 |
| 20 | FC Copenhagen | Drita | 1 : 0, 2 : 0 |
| 21 | Feyenoord | Bye | |
| 22 | Bye | Fenerbahce | |
| 23 | Nice | Bye | |
| 24 | Bye | Benfica | |
| 25 | Rangers | Panathinaikos | 1 : 1, 2 : 0 |
| 26 | Plzen | Servette | 3 : 1, 0 : 1 |
| 27 | Brann | Salzburg | 1 : 1, 1 : 4 |
| 28 | Bye | Club Brugge KV |
Semi-finals
| 1 | Ludogorets | Ferencvaros | 0 : 3, 0 : 0 |
| 2 | Shkendija | Qarabag | 1 : 5, 0 : 1 |
| 3 | Lech Poznan | Crvena zvezda | 1 : 1, 1 : 3 |
| 4 | Dyn. Kyiv | Pafos | 0 : 2, 0 : 1 |
| 5 | Bodo/Glimt | Bye | |
| 6 | Bye | Sturm Graz | |
| 7 | Celtic | Bye | |
| 8 | Kairat Almaty | Slovan Bratislava | 1 : 1, 1 : 0 |
| 9 | Basel | Bye | |
| 10 | Malmo FF | FC Copenhagen | 0 : 5, 0 : 0 |
| 11 | Feyenoord | Fenerbahce | 2 : 5, 2 : 1 |
| 12 | Nice | Benfica | 0 : 2, 0 : 2 |
| 13 | Rangers | Plzen | 1 : 2, 3 : 0 |
| 14 | Salzburg | Club Brugge KV | 2 : 3, 0 : 1 |
Final
| 1 | Ferencvaros | Qarabag | 1 : 3 |
| 2 | Crvena zvezda | Pafos | 1 : 1, 1 : 2 |
| 3 | Bodo/Glimt | Sturm Graz | 1 : 2, 5 : 0 |
| 4 | Celtic | Kairat Almaty | 0 : 1, 0 : 0 |
| 5 | Basel | FC Copenhagen | 1 : 1 |
| 6 | Fenerbahce | Benfica | 0 : 0 |
| 7 | Rangers | Club Brugge KV | 1 : 3 |
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