Draw
2025/261/8-finals
| 1 | Fredrikstad | Bye | |
| 3 | Midtjylland | Bye | |
| 4 | Bye | Hibernian | |
| 5 | PAOK | Bye | |
| 8 | Bye | Wolfsberger AC | |
| 9 | Sabah Baku | Celje | 3 : 3, 2 : 3 |
| 10 | AEK Larnaca | Partizan | 2 : 2, 1 : 0 |
| 11 | Ostrava | Bye | |
| 12 | Legia | Aktobe | 1 : 0, 1 : 0 |
| 13 | Lugano | Bye | |
| 14 | Paks | CFR Cluj | 0 : 3, 0 : 0 |
| 15 | Levski Sofia | H. Beer Sheva | 2 : 1, 0 : 0 |
| 16 | Bye | Braga | |
| 19 | Sheriff Tiraspol | Prishtina | 1 : 2, 4 : 0 |
| 20 | Bye | Utrecht | |
| 21 | Anderlecht | Bye | |
| 22 | Trnava | Hacken | 2 : 2, 0 : 1 |
| 27 | Besiktas | Bye | |
| 28 | Shakhtar Donetsk | Ilves | 0 : 0, 6 : 0 |
Quarter-finals
| 1 | Fredrikstad | Bye | |
| 2 | Midtjylland | Hibernian | 1 : 1 |
| 3 | PAOK | Bye | |
| 4 | Bye | Wolfsberger AC | |
| 5 | Celje | AEK Larnaca | 1 : 1 |
| 6 | Ostrava | Legia | 2 : 2 |
| 7 | Lugano | CFR Cluj | 0 : 0 |
| 8 | Levski Sofia | Braga | 0 : 0 |
| 10 | Sheriff Tiraspol | Utrecht | 1 : 3 |
| 11 | Anderlecht | Hacken | 1 : 0 |
| 14 | Besiktas | Shakhtar Donetsk | 2 : 4 |
Semi-finals
| 1 | Fredrikstad | TBD #2 | |
| 2 | PAOK | Wolfsberger AC | |
| 3 | TBD #5 | TBD #6 | |
| 4 | TBD #7 | TBD #8 | |
| 5 | Bye | TBD #10 | |
| 6 | TBD #11 | Bye | |
| 7 | Bye | TBD #14 |
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