| Group B | 04/10/2012 | Atlético Madrid | - | Viktoria Plzeň | 1:0 | ||||
| Group B | 25/10/2012 | Hapoel Tel Aviv | - | Viktoria Plzeň | 1:2 | ||||
| Group B | 08/11/2012 | Viktoria Plzeň | - | Hapoel Tel Aviv | 4:0 |  |
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| Group B | 22/11/2012 | Académica de Coimbra | - | Viktoria Plzeň | 1:1 | ||||
| Group B | 06/12/2012 | Viktoria Plzeň | - | Atlético Madrid | 1:0 | ||||
| 2. Round | 14/02/2013 | SSC Napoli | - | Viktoria Plzeň | 0:3 | ||||
| 2. Round | 21/02/2013 | Viktoria Plzeň | - | SSC Napoli | 2:0 |  |
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| Round of 16 | 07/03/2013 | Viktoria Plzeň | - | Fenerbahçe | 0:1 | ||||
| Round of 16 | 14/03/2013 | Fenerbahçe | - | Viktoria Plzeň | 1:1 | |
Slovakia