1. Round | 06/08/2016 | Hartlepool United | - | Colchester United | 1:1 | ||||
2. Round | 13/08/2016 | Colchester United | - | Cambridge United | 2:0 | ||||
3. Round | 16/08/2016 | Colchester United | - | Grimsby Town | 3:2 | ||||
4. Round | 20/08/2016 | Portsmouth FC | - | Colchester United | 2:0 | ||||
5. Round | 27/08/2016 | Wycombe Wanderers | - | Colchester United | 0:2 | ||||
6. Round | 03/09/2016 | Colchester United | - | Exeter City | 2:3 | ||||
7. Round | 10/09/2016 | Colchester United | - | Blackpool FC | 3:2 | ||||
8. Round | 17/09/2016 | Barnet FC | - | Colchester United | 1:1 | ||||
9. Round | 24/09/2016 | Colchester United | - | Accrington Stanley | 1:2 | ||||
10. Round | 27/09/2016 | Crawley Town | - | Colchester United | 1:1 | ||||
11. Round | 01/10/2016 | Carlisle United | - | Colchester United | 2:0 | ||||
13. Round | 15/10/2016 | Doncaster Rovers | - | Colchester United | 1:0 | ||||
14. Round | 22/10/2016 | Colchester United | - | Morecambe FC | 2:2 | ||||
15. Round | 29/10/2016 | Plymouth Argyle | - | Colchester United | 2:1 | ||||
16. Round | 12/11/2016 | Colchester United | - | Leyton Orient | 0:3 |