| 1. |  | AFK Atl. Lázně Bohdaneč | 30 | 2 | 5 | 23 | 18 | 61 | -43 | 11 |
| 2. |  | FK ŠVARC Benešov | 30 | 3 | 3 | 24 | 23 | 78 | -55 | 12 |
| 3. |  | MFK Vítkovice | 30 | 3 | 7 | 20 | 22 | 64 | -42 | 13 |
| 4. |  | FC JOKO Slovácká Slavia Uherské Hradiště | 30 | 3 | 8 | 19 | 19 | 65 | -46 | 17 |
| 5. |  | FK Ústí nad Labem | 30 | 4 | 7 | 19 | 22 | 67 | -45 | 19 |
| 6. |  | 1.SC Znojmo FK | 30 | 6 | 9 | 15 | 32 | 49 | -17 | 27 |
| 7. |  | FK Bohemians Praha | 60 | 14 | 8 | 38 | 60 | 111 | -51 | 50 |
| 8. |  | FC Karviná | 60 | 12 | 12 | 36 | 53 | 105 | -52 | 48 |
| 9. |  | FK SIAD Most | 90 | 19 | 30 | 41 | 96 | 140 | -44 | 87 |
| 10. |  | FC Union Cheb | 90 | 29 | 26 | 35 | 95 | 121 | -26 | 100 |
| 11. |  | SK Kladno | 120 | 28 | 30 | 62 | 99 | 173 | -74 | 114 |
| 12. |  | FC Vysočina Jihlava | 210 | 55 | 61 | 94 | 221 | 315 | -94 | 226 |
| 13. |  | FK Chmel Blšany | 240 | 67 | 63 | 110 | 255 | 350 | -95 | 264 |
| 14. |  | FK Pardubice | 290 | 82 | 62 | 146 | 319 | 505 | -186 | 308 |
| 15. |  | FK Dukla Praha | 310 | 82 | 83 | 145 | 355 | 492 | -137 | 328 |
| 16. |  | MFK Karviná | 416 | 77 | 113 | 226 | 417 | 665 | -248 | 344 |
| 17. |  | FK Drnovice | 300 | 114 | 67 | 119 | 392 | 398 | -6 | 396 |
| 18. |  | Slezský FC Opava | 440 | 105 | 114 | 221 | 427 | 686 | -259 | 429 |
| 19. |  | FK Viktoria Žižkov | 420 | 144 | 106 | 170 | 478 | 539 | -61 | 526 |
| 20. |  | FC Hradec Králové | 674 | 189 | 189 | 296 | 674 | 949 | -275 | 747 |
| 21. |  | FK VIAGEM Příbram | 770 | 213 | 192 | 365 | 780 | 1168 | -388 | 831 |
| 22. |  | FC Zlín | 844 | 226 | 224 | 394 | 878 | 1284 | -406 | 892 |
| 23. |  | FC Zbrojovka Brno | 854 | 271 | 222 | 361 | 995 | 1189 | -194 | 1025 |
| 24. |  | SK Dynamo České Budějovice | 912 | 270 | 226 | 416 | 1019 | 1424 | -405 | 1025 |
| 25. |  | Bohemians Praha 1905 | 938 | 279 | 261 | 398 | 1036 | 1341 | -305 | 1090 |
| 26. |  | FK Mladá Boleslav | 872 | 341 | 225 | 306 | 1320 | 1207 | +113 | 1248 |
| 27. |  | 1.FC Slovácko | 934 | 348 | 235 | 351 | 1134 | 1154 | -20 | 1279 |
| 28. |  | FK Teplice | 1110 | 372 | 306 | 432 | 1326 | 1511 | -185 | 1422 |
| 29. |  | SK Sigma Olomouc | 1138 | 417 | 329 | 392 | 1467 | 1363 | +104 | 1566 |
| 30. |  | FC Baník Ostrava | 1217 | 434 | 344 | 439 | 1638 | 1549 | +89 | 1632 |
| 31. |  | FK Jablonec | 1180 | 434 | 343 | 403 | 1567 | 1489 | +78 | 1645 |
| 32. |  | FC Slovan Liberec | 1239 | 513 | 325 | 401 | 1663 | 1438 | +225 | 1853 |
| 33. |  | FC Viktoria Plzeň | 1090 | 578 | 243 | 269 | 1766 | 1124 | +642 | 1965 |
| 34. |  | SK Slavia Praha | 1210 | 710 | 286 | 214 | 2257 | 1025 | +1232 | 2400 |
| 35. |  | AC Sparta Praha | 1210 | 755 | 256 | 199 | 2335 | 1059 | +1276 | 2503 |
