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| 03/09/2016 | 09:15 | FK Baník Sokolov | - | Dynamo České Budějovice | 1:1 (0:1) | |
| 09:15 | FK Fotbal Třinec | - | MFK Vítkovice | 2:1 (2:1) | ||
| 16:00 | MFK Frýdek-Místek, a.s. | - | 1. SK Prostějov | 2:2 (1:2) | ||
| 04/09/2016 | 16:00 | FK Varnsdorf | - | Viktoria Žižkov | 0:0 (0:0) | |
| 07/09/2016 | 16:00 | 1. SC Znojmo | - | FK Pardubice | 5:2 (2:2) | |
| 13/09/2016 | 17:00 | FK Ústí nad Labem | - | FC Sellier & Bellot Vlašim | 2:5 (1:2) | |
| 14/09/2016 | 18:00 | Baník Ostrava | - | SFC Opava | 3:0 (1:0) | |
| 04/10/2016 | 16:00 | Sigma Olomouc | - | FK MAS Táborsko | 2:0 (1:0) |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Baník Ostrava | 5 | 4 | 1 | 0 | 11:3 | 8 | 13 |
| 2 |
|
Dynamo České Budějovice | 5 | 3 | 2 | 0 | 5:1 | 4 | 11 |
| 3 |
|
Sigma Olomouc | 5 | 2 | 3 | 0 | 6:3 | 3 | 9 |
| 4 |
|
FK Varnsdorf | 5 | 2 | 2 | 1 | 4:1 | 3 | 8 |
| 5 |
|
SFC Opava | 5 | 2 | 2 | 1 | 9:7 | 2 | 8 |
| 6 |
|
1. SC Znojmo | 5 | 2 | 1 | 2 | 11:9 | 2 | 7 |
| 7 |
|
MFK Frýdek-Místek, a.s. | 5 | 2 | 1 | 2 | 8:9 | -1 | 7 |
| 8 |
|
FK MAS Táborsko | 5 | 2 | 1 | 2 | 5:6 | -1 | 7 |
| 9 |
|
Viktoria Žižkov | 5 | 1 | 3 | 1 | 9:7 | 2 | 6 |
| 10 |
|
FK Baník Sokolov | 5 | 1 | 3 | 1 | 5:7 | -2 | 6 |
| 11 |
|
MFK Vítkovice | 5 | 2 | 0 | 3 | 4:7 | -3 | 6 |
| 12 |
|
FK Pardubice | 5 | 1 | 2 | 2 | 6:11 | -5 | 5 |
| 13 |
|
FC Sellier & Bellot Vlašim | 5 | 1 | 1 | 3 | 9:11 | -2 | 4 |
| 14 |
|
FK Fotbal Třinec | 5 | 1 | 1 | 3 | 9:12 | -3 | 4 |
| 15 |
|
FK Ústí nad Labem | 5 | 1 | 1 | 3 | 7:11 | -4 | 4 |
| 16 |
|
1. SK Prostějov | 5 | 0 | 2 | 3 | 4:7 | -3 | 2 |
| Promotion | |
| Relegation |
