| 1er tour | 04.07.2013 | FC Flora | - | FK Kukësi | 1:1 | ||||
| 1er tour | 11.07.2013 | FK Kukësi | - | FC Flora | 0:0 | ||||
| 2e tour | 25.07.2013 | FK Sarajevo | - | FK Kukësi | 0:0 | ||||
| 3e tour | 01.08.2013 | FK Kukësi | - | Metalurh Donetsk | 2:0 | ||||
| 3e tour | 08.08.2013 | Metalurh Donetsk | - | FK Kukësi | 1:0 | ||||
| Play-offs | 22.08.2013 | FK Kukësi | - | Trabzonspor | 0:2 |  |
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| Play-offs | 29.08.2013 | Trabzonspor | - | FK Kukësi | 3:1 |
Albanie