| 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 Dukla Praha | 324 | 86 | 85 | 153 | 365 | 508 | -143 | 342 |
| 15. |  | FK Pardubice | 348 | 101 | 69 | 178 | 384 | 587 | -203 | 372 |
| 16. |  | FK Drnovice | 300 | 114 | 67 | 119 | 392 | 398 | -6 | 396 |
| 17. |  | MFK Karviná | 474 | 93 | 128 | 253 | 479 | 761 | -282 | 407 |
| 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 | 732 | 212 | 201 | 319 | 738 | 1015 | -277 | 828 |
| 21. |  | FK VIAGEM Příbram | 770 | 213 | 192 | 365 | 780 | 1168 | -388 | 831 |
| 22. |  | FC Zlín | 888 | 231 | 240 | 417 | 922 | 1363 | -441 | 923 |
| 23. |  | FC Zbrojovka Brno | 854 | 271 | 222 | 361 | 995 | 1189 | -194 | 1025 |
| 24. |  | SK Dynamo České Budějovice | 970 | 278 | 242 | 450 | 1077 | 1548 | -471 | 1065 |
| 25. |  | Bohemians Praha 1905 | 996 | 295 | 280 | 421 | 1093 | 1415 | -322 | 1157 |
| 26. |  | 1.FC Slovácko | 992 | 365 | 255 | 372 | 1199 | 1242 | -43 | 1350 |
| 27. |  | FK Mladá Boleslav | 967 | 378 | 243 | 346 | 1459 | 1364 | +95 | 1377 |
| 28. |  | FK Teplice | 1166 | 387 | 317 | 462 | 1383 | 1599 | -216 | 1478 |
| 29. |  | SK Sigma Olomouc | 1190 | 433 | 342 | 415 | 1539 | 1452 | +87 | 1627 |
| 30. |  | FC Baník Ostrava | 1275 | 455 | 358 | 462 | 1726 | 1628 | +98 | 1709 |
| 31. |  | FK Jablonec | 1238 | 452 | 367 | 419 | 1638 | 1554 | +84 | 1723 |
| 32. |  | FC Slovan Liberec | 1291 | 527 | 343 | 421 | 1733 | 1512 | +221 | 1913 |
| 33. |  | FC Viktoria Plzeň | 1148 | 613 | 258 | 277 | 1889 | 1179 | +710 | 2085 |
| 34. |  | SK Slavia Praha | 1268 | 754 | 298 | 216 | 2381 | 1058 | +1323 | 2544 |
| 35. |  | AC Sparta Praha | 1268 | 801 | 266 | 201 | 2477 | 1113 | +1364 | 2651 |
