| 1. Round | 06/08/2016 | Southend United | - | Gillingham FC | 1:3 | ||||
| 2. Round | 13/08/2016 | Port Vale FC | - | Southend United | 2:0 | ||||
| 3. Round | 16/08/2016 | Sheffield United | - | Southend United | 0:3 | ||||
| 4. Round | 20/08/2016 | Southend United | - | Bristol Rovers | 1:1 | ||||
| 5. Round | 27/08/2016 | Southend United | - | Fleetwood Town | 0:2 | ||||
| 6. Round | 03/09/2016 | Bolton Wanderers | - | Southend United | 1:1 | ||||
| 16. Round | 29/10/2016 | Southend United | - | Shrewsbury Town | 1:1 |
England