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| 30/09/2016 | 15:00 | Sigma Olomouc | - | Viktoria Žižkov | 2:0 (1:0) | |
| 17:00 | FK Ústí nad Labem | - | FK MAS Táborsko | 0:0 (0:0) | ||
| 01/10/2016 | 09:05 | FK Baník Sokolov | - | FK Varnsdorf | 3:2 (0:0) | |
| 14:00 | Baník Ostrava | - | Dynamo České Budějovice | 3:2 (1:1) | ||
| 14:30 | MFK Frýdek-Místek, a.s. | - | MFK Vítkovice | 5:2 (2:0) | ||
| 15:30 | FC Sellier & Bellot Vlašim | - | FK Pardubice | 1:0 (0:0) | ||
| 18:00 | SFC Opava | - | 1. SK Prostějov | 3:1 (1:1) | ||
| 02/10/2016 | 17:00 | 1. SC Znojmo | - | FK Fotbal Třinec | 2:2 (1:2) |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Baník Ostrava | 9 | 6 | 3 | 0 | 18:6 | 12 | 21 |
| 2 |
|
Sigma Olomouc | 9 | 6 | 3 | 0 | 14:4 | 10 | 21 |
| 3 |
|
SFC Opava | 9 | 5 | 3 | 1 | 19:12 | 7 | 18 |
| 4 |
|
Dynamo České Budějovice | 9 | 5 | 2 | 2 | 12:7 | 5 | 17 |
| 5 |
|
FK Baník Sokolov | 9 | 4 | 4 | 1 | 13:12 | 1 | 16 |
| 6 |
|
1. SC Znojmo | 9 | 4 | 3 | 2 | 19:14 | 5 | 15 |
| 7 |
|
FK Varnsdorf | 9 | 3 | 3 | 3 | 11:11 | 0 | 12 |
| 8 |
|
Viktoria Žižkov | 9 | 2 | 5 | 2 | 16:15 | 1 | 11 |
| 9 |
|
FC Sellier & Bellot Vlašim | 9 | 3 | 2 | 4 | 15:14 | 1 | 11 |
| 10 |
|
MFK Frýdek-Místek, a.s. | 9 | 3 | 2 | 4 | 17:18 | -1 | 11 |
| 11 |
|
FK Ústí nad Labem | 9 | 3 | 2 | 4 | 12:13 | -1 | 11 |
| 12 |
|
FK MAS Táborsko | 9 | 2 | 4 | 3 | 9:11 | -2 | 10 |
| 13 |
|
FK Fotbal Třinec | 9 | 1 | 3 | 5 | 14:20 | -6 | 6 |
| 14 |
|
MFK Vítkovice | 9 | 2 | 0 | 7 | 10:19 | -9 | 6 |
| 15 |
|
FK Pardubice | 9 | 1 | 3 | 5 | 6:16 | -10 | 6 |
| 16 |
|
1. SK Prostějov | 9 | 0 | 2 | 7 | 5:18 | -13 | 2 |
| Promotion | |
| Relegation |
