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| 02/11/2016 | 16:00 | Sigma Olomouc | - | FK Ústí nad Labem | 5:0 (3:0) | |
| 04/11/2016 | 16:30 | 1. SC Znojmo | - | MFK Frýdek-Místek, a.s. | 0:2 (0:0) | |
| 05/11/2016 | 09:15 | FK Fotbal Třinec | - | FK Pardubice | 1:0 (1:0) | |
| 09:15 | FK Baník Sokolov | - | Baník Ostrava | 0:0 (0:0) | ||
| 13:00 | MFK Vítkovice | - | FC Sellier & Bellot Vlašim | 0:2 (0:2) | ||
| 13:00 | FK MAS Táborsko | - | Dynamo České Budějovice | 0:1 (0:1) | ||
| 06/11/2016 | 09:15 | Viktoria Žižkov | - | 1. SK Prostějov | 5:1 (3:1) | |
| 13:00 | FK Varnsdorf | - | SFC Opava | 1:0 (1:0) |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Sigma Olomouc | 14 | 10 | 4 | 0 | 26:8 | 18 | 34 |
| 2 |
|
Baník Ostrava | 14 | 8 | 6 | 0 | 23:9 | 14 | 30 |
| 3 |
|
SFC Opava | 14 | 8 | 3 | 3 | 30:15 | 15 | 27 |
| 4 |
|
Dynamo České Budějovice | 14 | 8 | 3 | 3 | 19:10 | 9 | 27 |
| 5 |
|
FC Sellier & Bellot Vlašim | 14 | 8 | 2 | 4 | 24:16 | 8 | 26 |
| 6 |
|
1. SC Znojmo | 14 | 6 | 3 | 5 | 24:20 | 4 | 21 |
| 7 |
|
Viktoria Žižkov | 14 | 5 | 5 | 4 | 24:18 | 6 | 20 |
| 8 |
|
MFK Frýdek-Místek, a.s. | 14 | 5 | 5 | 4 | 27:23 | 4 | 20 |
| 9 |
|
FK Ústí nad Labem | 14 | 6 | 2 | 6 | 17:21 | -4 | 20 |
| 10 |
|
FK Baník Sokolov | 14 | 4 | 6 | 4 | 18:21 | -3 | 18 |
| 11 |
|
FK Varnsdorf | 14 | 4 | 4 | 6 | 14:17 | -3 | 16 |
| 12 |
|
FK MAS Táborsko | 14 | 3 | 5 | 6 | 14:23 | -9 | 14 |
| 13 |
|
FK Fotbal Třinec | 14 | 3 | 3 | 8 | 19:32 | -13 | 12 |
| 14 |
|
FK Pardubice | 14 | 2 | 5 | 7 | 8:20 | -12 | 11 |
| 15 |
|
MFK Vítkovice | 14 | 2 | 0 | 12 | 12:27 | -15 | 6 |
| 16 |
|
1. SK Prostějov | 14 | 1 | 2 | 11 | 11:30 | -19 | 5 |
| Promotion | |
| Relegation |
