| 1 | FK DUKLA Praha a.s. | 28 | 17 | 5 | 6 | 56 | 49:29 | 20 |
| 2 | SK Sigma Olomouc, a.s. B | 28 | 16 | 3 | 9 | 51 | 44:36 | 8 |
| 3 | MFK Vyškov a.s. | 28 | 13 | 7 | 8 | 46 | 45:36 | 9 |
| 4 | FC SILON Táborsko a.s. | 28 | 12 | 9 | 7 | 45 | 39:26 | 13 |
| 5 | MFK Chrudim a.s. | 28 | 10 | 9 | 9 | 39 | 46:44 | 2 |
| 6 | SK Líšeň 2019, a.s. | 28 | 9 | 11 | 8 | 38 | 33:32 | 1 |
| 7 | FC Sellier & Bellot Vlašim, a.s. | 28 | 9 | 11 | 8 | 38 | 37:39 | -2 |
| 8 | Slezský fotbalový club Opava a.s. | 28 | 10 | 7 | 11 | 37 | 31:32 | -1 |
| 9 | AC Sparta Praha fotbal, a.s. B | 28 | 10 | 6 | 12 | 36 | 50:50 | 0 |
| 10 | FK VIKTORIA ŽIŽKOV a.s. | 28 | 10 | 6 | 12 | 36 | 42:48 | -6 |
| 11 | FC VYSOČINA JIHLAVA, a.s. | 28 | 9 | 8 | 11 | 35 | 40:40 | 0 |
| 12 | FC ZBROJOVKA BRNO, a.s. | 28 | 10 | 5 | 13 | 35 | 35:37 | -2 |
| 13 | FK PŘÍBRAM a.s. | 28 | 10 | 4 | 14 | 34 | 30:42 | -12 |
| 14 | Fotbalový klub Varnsdorf a.s. | 28 | 7 | 12 | 9 | 33 | 49:48 | 1 |
| 15 | 1. SK Prostějov, fotbalový klub a.s. | 28 | 9 | 4 | 15 | 31 | 37:51 | -14 |
| 16 | SK Hanácká Slavia Kroměříž a.s. | 28 | 6 | 7 | 15 | 25 | 30:47 | -17 |
