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| 30.03.2013 | 10:15 | FK Pardubice | - | FC Graffin Vlašim | 2:1 (1:0) | |
| 10:15 | Bohemians Praha | - | FK Ústí nad Labem | 1:1 (0:1) | ||
| 10:15 | FK Baník Sokolov | - | 1. SC Znojmo | 0:0 (0:0) | ||
| 14:30 | FK Baník Most | - | FK Čáslav | 2:1 (0:1) | ||
| 15:00 | 1. HFK Olomouc | - | Viktoria Žižkov | 0:0 (0:0) | ||
| 17:00 | FC Fastav Zlín | - | FK MAS Táborsko | 3:2 (0:1) | ||
| 31.03.2013 | 17:00 | Bohemians 1905 | - | SFC Opava | 1:0 (1:0) | |
| 17.05.2013 | 17:00 | MFK Karviná | - | FK Varnsdorf | 2:1 (1:0) |
| # | Mannschaft | Sp. | S. | U. | N. | Tore | Dif. | Pk. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Bohemians 1905 | 21 | 11 | 6 | 4 | 32:17 | 15 | 39 |
| 2 |
|
1. SC Znojmo | 21 | 11 | 5 | 5 | 28:19 | 9 | 38 |
| 3 |
|
1. HFK Olomouc | 21 | 11 | 4 | 6 | 30:24 | 6 | 37 |
| 4 |
|
FK Varnsdorf | 21 | 11 | 3 | 7 | 37:23 | 14 | 36 |
| 5 |
|
FK Baník Sokolov | 21 | 9 | 7 | 5 | 26:18 | 8 | 34 |
| 6 |
|
FK Pardubice | 21 | 10 | 3 | 8 | 34:23 | 11 | 33 |
| 7 |
|
FC Fastav Zlín | 21 | 10 | 3 | 8 | 33:26 | 7 | 33 |
| 8 |
|
Viktoria Žižkov | 21 | 9 | 6 | 6 | 25:18 | 7 | 33 |
| 9 |
|
FK Ústí nad Labem | 21 | 8 | 6 | 7 | 23:29 | -6 | 30 |
| 10 |
|
Bohemians Praha | 21 | 3 | 14 | 4 | 18:19 | -1 | 23 |
| 11 |
|
MFK Karviná | 21 | 5 | 8 | 8 | 21:32 | -11 | 23 |
| 12 |
|
FC Graffin Vlašim | 21 | 6 | 4 | 11 | 26:37 | -11 | 22 |
| 13 |
|
FK Baník Most | 21 | 5 | 6 | 10 | 23:36 | -13 | 21 |
| 14 |
|
FK MAS Táborsko | 21 | 4 | 8 | 9 | 19:28 | -9 | 20 |
| 15 |
|
SFC Opava | 21 | 4 | 6 | 11 | 20:34 | -14 | 18 |
| 16 |
|
FK Čáslav | 21 | 3 | 7 | 11 | 13:25 | -12 | 16 |
| Aufstieg | |
| Abstieg |
