| 6. Round | 03/09/2016 | Bolton Wanderers | - | Southend United | 1:1 | ||||
| 7. Round | 10/09/2016 | Scunthorpe United | - | Southend United | 4:0 | ||||
| 8. Round | 17/09/2016 | Southend United | - | Millwall FC | 3:1 | ||||
| 9. Round | 24/09/2016 | Northampton Town | - | Southend United | 4:0 |  |
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| 17. Round | 12/11/2016 | Bury FC | - | Southend United | 1:4 | ||||
| 29. Round | 28/01/2017 | Fleetwood Town | - | Southend United | 1:1 | ||||
| 34. Round | 25/02/2017 | Gillingham FC | - | Southend United | 2:1 | ||||
| 38. Round | 14/03/2017 | Coventry City | - | Southend United | 0:2 | ||||
| 39. Round | 18/03/2017 | Southend United | - | Walsall FC | 3:2 | ||||
| 28. Round | 04/04/2017 | Southend United | - | Bolton Wanderers | 0:1 | ||||
| 42. Round | 08/04/2017 | Charlton Athletic | - | Southend United | 2:1 |  |
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| 43. Round | 14/04/2017 | Chesterfield FC | - | Southend United | 0:4 | ||||
| 45. Round | 22/04/2017 | Shrewsbury Town | - | Southend United | 1:0 |
England