| 1. Runde | 04.07.2013 | VMFD Žalgiris | - | St Patrick's Athletic | 2:2 | ||||
| 1. Runde | 11.07.2013 | St Patrick's Athletic | - | VMFD Žalgiris | 1:2 |  |
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| 2. Runde | 18.07.2013 | VMFD Žalgiris | - | Pyunik FC | 2:0 | ||||
| 2. Runde | 25.07.2013 | Pyunik FC | - | VMFD Žalgiris | 1:1 | ||||
| 3. Runde | 01.08.2013 | VMFD Žalgiris | - | Lech Poznań | 1:0 | ||||
| 3. Runde | 08.08.2013 | Lech Poznań | - | VMFD Žalgiris | 2:1 | ||||
| Playoffs | 22.08.2013 | RB Salzburg | - | VMFD Žalgiris | 5:0 | ||||
| Playoffs | 29.08.2013 | VMFD Žalgiris | - | RB Salzburg | 0:2 |
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