| 5. Jornada | 27.08.2016 | Wycombe Wanderers | - | Colchester United | 0:2 | ||||
| 12. Jornada | 08.10.2016 | Colchester United | - | Newport County | 0:0 | ||||
| 13. Jornada | 15.10.2016 | Doncaster Rovers | - | Colchester United | 1:0 | ||||
| 14. Jornada | 22.10.2016 | Colchester United | - | Morecambe FC | 2:2 | ||||
| 15. Jornada | 29.10.2016 | Plymouth Argyle | - | Colchester United | 2:1 |  |
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| 16. Jornada | 12.11.2016 | Colchester United | - | Leyton Orient | 0:3 | ||||
| 17. Jornada | 19.11.2016 | Yeovil Town | - | Colchester United | 2:1 | ||||
| 30. Jornada | 11.02.2017 | Colchester United | - | Barnet FC | 2:1 | ||||
| 31. Jornada | 14.02.2017 | Colchester United | - | Crawley Town | 2:3 | ||||
| 32. Jornada | 18.02.2017 | Accrington Stanley | - | Colchester United | 2:1 | |
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| 37. Jornada | 14.03.2017 | Colchester United | - | Mansfield Town | 2:0 | ||||
| 39. Jornada | 25.03.2017 | Colchester United | - | Luton Town | 2:1 | ||||
| 43. Jornada | 17.04.2017 | Morecambe FC | - | Colchester United | 1:1 | ||||
| 45. Jornada | 29.04.2017 | Leyton Orient | - | Colchester United | 1:3 | ||||
| 46. Jornada | 06.05.2017 | Colchester United | - | Yeovil Town | 2:0 |
Inglaterra