| 1. |  | AFK Atl. Lázně Bohdaneč | 30 | 2 | 5 | 23 | 18 | 61 | -43 | 11 |
| 2. |  | FC JOKO Slovácká Slavia Uherské Hradiště | 30 | 3 | 8 | 19 | 19 | 65 | -46 | 17 |
| 3. |  | MFK Vítkovice | 30 | 3 | 7 | 20 | 22 | 64 | -42 | 13 |
| 4. |  | FK Ústí nad Labem | 30 | 4 | 7 | 19 | 22 | 67 | -45 | 19 |
| 5. |  | FK ŠVARC Benešov | 30 | 3 | 3 | 24 | 23 | 78 | -55 | 12 |
| 6. |  | 1.SC Znojmo FK | 30 | 6 | 9 | 15 | 32 | 49 | -17 | 27 |
| 7. |  | FC Karviná | 60 | 12 | 12 | 36 | 53 | 105 | -52 | 48 |
| 8. |  | FK Bohemians Praha | 60 | 14 | 8 | 38 | 60 | 111 | -51 | 50 |
| 9. |  | FC Union Cheb | 90 | 29 | 26 | 35 | 95 | 121 | -26 | 100 |
| 10. |  | FK SIAD Most | 90 | 19 | 30 | 41 | 96 | 140 | -44 | 87 |
| 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 | 310 | 82 | 83 | 145 | 355 | 492 | -137 | 328 |
| 15. |  | FK Pardubice | 330 | 93 | 69 | 168 | 362 | 565 | -203 | 348 |
| 16. |  | FK Drnovice | 300 | 114 | 67 | 119 | 392 | 398 | -6 | 396 |
| 17. |  | Slezský FC Opava | 440 | 105 | 114 | 221 | 427 | 686 | -259 | 429 |
| 18. |  | MFK Karviná | 456 | 87 | 124 | 245 | 465 | 731 | -266 | 385 |
| 19. |  | FK Viktoria Žižkov | 420 | 144 | 106 | 170 | 478 | 539 | -61 | 526 |
| 20. |  | FC Hradec Králové | 712 | 202 | 201 | 309 | 720 | 995 | -275 | 798 |
| 21. |  | FK VIAGEM Příbram | 770 | 213 | 192 | 365 | 780 | 1168 | -388 | 831 |
| 22. |  | FC Zlín | 884 | 231 | 240 | 413 | 920 | 1357 | -437 | 923 |
| 23. |  | FC Zbrojovka Brno | 854 | 271 | 222 | 361 | 995 | 1189 | -194 | 1025 |
| 24. |  | SK Dynamo České Budějovice | 952 | 278 | 238 | 436 | 1071 | 1504 | -433 | 1061 |
| 25. |  | Bohemians Praha 1905 | 978 | 289 | 276 | 413 | 1077 | 1397 | -320 | 1135 |
| 26. |  | 1.FC Slovácko | 974 | 361 | 247 | 366 | 1189 | 1216 | -27 | 1330 |
| 27. |  | FK Teplice | 1148 | 385 | 317 | 446 | 1369 | 1563 | -194 | 1472 |
| 28. |  | FK Mladá Boleslav | 912 | 357 | 235 | 320 | 1378 | 1265 | +113 | 1306 |
| 29. |  | SK Sigma Olomouc | 1176 | 427 | 338 | 411 | 1517 | 1432 | +85 | 1605 |
| 30. |  | FK Jablonec | 1220 | 444 | 361 | 415 | 1618 | 1542 | +76 | 1693 |
| 31. |  | FC Baník Ostrava | 1257 | 447 | 352 | 458 | 1698 | 1616 | +82 | 1679 |
| 32. |  | FC Slovan Liberec | 1277 | 523 | 339 | 415 | 1715 | 1496 | +219 | 1897 |
| 33. |  | FC Viktoria Plzeň | 1130 | 603 | 250 | 277 | 1855 | 1169 | +686 | 2047 |
| 34. |  | SK Slavia Praha | 1250 | 738 | 296 | 216 | 2343 | 1054 | +1289 | 2494 |
| 35. |  | AC Sparta Praha | 1250 | 787 | 262 | 201 | 2433 | 1099 | +1334 | 2605 |
