| 31. Round | 02/02/2019 | Northampton Town | - | Colchester United | 0:4 |  |
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| 32. Round | 09/02/2019 | Colchester United | - | Cheltenham Town | 3:0 | |
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| 33. Round | 16/02/2019 | Macclesfield Town | - | Colchester United | 1:1 | ||||
| 34. Round | 23/02/2019 | Colchester United | - | Carlisle United | 1:1 | ||||
| 36. Round | 09/03/2019 | Colchester United | - | Newport County | 3:0 | ||||
| 37. Round | 12/03/2019 | Colchester United | - | Forest Green Rovers | 0:3 | ||||
| 38. Round | 16/03/2019 | Exeter City | - | Colchester United | 3:0 | ||||
| 39. Round | 23/03/2019 | Colchester United | - | Tranmere Rovers | 0:2 | ||||
| 40. Round | 30/03/2019 | Cambridge United | - | Colchester United | 0:1 | ||||
| 41. Round | 06/04/2019 | Colchester United | - | Oldham Athletic | 0:2 | ||||
| 43. Round | 19/04/2019 | Colchester United | - | Grimsby Town | 1:0 | ||||
| 44. Round | 22/04/2019 | Yeovil Town | - | Colchester United | 1:1 | ||||
| 45. Round | 27/04/2019 | Colchester United | - | Milton Keynes Dons | 2:0 | ||||
| 46. Round | 04/05/2019 | Lincoln City | - | Colchester United | 0:3 |
Sudan