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| 24.08.2016 | 17:00 | Tartu Ülikool Fauna | - | EMÜ SK | 4:6 | |
| 01.09.2016 | 17:00 | Tulevik Viljandi | - | JK Sillamäe Kalev | 1:0 (0:0) | |
| 18:00 | Saue JK Laagri | - | FC Infonet II | 0:3 (0:1) | ||
| 04.09.2016 | 11:00 | JK Terav Sats | - | Raplamaa JK II | 0:2 (0:0) | |
| 13:00 | FC Kuressaare | - | Tallinna JK Legion | 3:2 | ||
| 15:30 | Rumori Calcio | - | JK Kernu Kadakas | 4:3 (3:2) | ||
| 06.09.2016 | 17:00 | FC Tartu | - | FC Infonet | 0:11 (0:4) | |
| 07.09.2016 | 16:30 | JK Tallinna Kalev | - | SK Tääksi | 5:0 (4:0) | |
| 20.09.2016 | 16:00 | Rakvere JK Tarvas | - | Paide Linnameeskond | 2:3 (0:1) | |
| 18:00 | FCI Levadia III | - | JK Tammeka | 1:8 (0:1) | ||
| 21.09.2016 | 16:00 | FC Molycorp Silmet | - | FC Flora III | 6:5 (0:3, 4:4) n.V. | |
| 16:00 | Kohtla-Järve JK Järve | - | FC Flora II | 0:2 (0:0) | ||
| 18:30 | Narva United FC | - | Viimsi JK | 3:2 (0:0, 0:0, 0:0) i.E. | ||
| 27.09.2016 | 18:00 | FC Levadia | - | Raasiku FC Joker | 7:0 (3:0) | |
| 28.09.2016 | 18:00 | FC Flora | - | Tõrva JK | 5:0 (0:0) | |
| 05.10.2016 | 17:00 | JK Nõmme Kalju | - | Pärnu JK Poseidon | 10:0 (5:0) |
