| 2. Round | 13/08/2016 | Port Vale FC | - | Southend United | 2:0 |  |
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| 6. Round | 03/09/2016 | Bolton Wanderers | - | Southend United | 1:1 | ||||
| 7. Round | 10/09/2016 | Scunthorpe United | - | Southend United | 4:0 | |
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| 17. Round | 12/11/2016 | Bury FC | - | Southend United | 1:4 | ||||
| 21. Round | 10/12/2016 | Southend United | - | Coventry City | 3:1 |
Czech Republic