| Group | Team | P | W | D | L | GD | PTS |
|---|---|---|---|---|---|---|---|
| FNL |  FC Zlin |
13 | 8 | 4 | 1 | 11 | 28 |
| FNL |  FC Zbrojovka Brno |
13 | 6 | 5 | 2 | 9 | 23 |
| FNL |  Sparta Prague B |
13 | 6 | 5 | 2 | 5 | 23 |
| FNL |  FK Varnsdorf |
13 | 6 | 3 | 4 | 3 | 21 |
| FNL |  FK MAS Taborsko |
13 | 6 | 2 | 5 | 4 | 20 |
| FNL |  Vysocina Jihlava |
13 | 5 | 5 | 3 | 4 | 20 |
| FNL |  MFK Chrudim |
13 | 5 | 5 | 3 | 4 | 20 |
| FNL |  SK Lisen |
13 | 5 | 4 | 4 | -2 | 19 |
| FNL |  Vyskov |
13 | 4 | 4 | 5 | 1 | 16 |
| FNL |  Banik Ostrava B |
13 | 4 | 4 | 5 | 1 | 16 |
| FNL |  FC Vlasim |
13 | 4 | 4 | 5 | 0 | 16 |
| FNL |  Opava |
13 | 4 | 4 | 5 | -2 | 16 |
| FNL |  SK Prostejov |
13 | 4 | 3 | 6 | -6 | 15 |
| FNL |  Slavia Prague B |
13 | 3 | 5 | 5 | -1 | 14 |
| FNL |  Zizkov |
13 | 4 | 1 | 8 | -8 | 13 |
| FNL |  Sigma Olomouc B |
13 | 0 | 2 | 11 | -23 | 2 |
- P: Played
- W: Wins
- D: Draws
- L: Losses
- GD: Goal Difference
- PTS: Points
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