| 1. Round | 06/08/2016 | Grimsby Town | - | Morecambe FC | 2:0 | ||||
| 2. Round | 13/08/2016 | Wycombe Wanderers | - | Grimsby Town | 2:1 |  |
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| 3. Round | 16/08/2016 | Colchester United | - | Grimsby Town | 3:2 |  |
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| 5. Round | 27/08/2016 | Grimsby Town | - | Stevenage FC | 5:2 | ||||
| 10. Round | 27/09/2016 | Grimsby Town | - | Newport County | 1:0 | ||||
| 22. Round | 26/12/2016 | Grimsby Town | - | Accrington Stanley | 2:0 | ||||
| 24. Round | 02/01/2017 | Carlisle United | - | Grimsby Town | 1:3 | ||||
| 25. Round | 07/01/2017 | Hartlepool United | - | Grimsby Town | 0:1 | ||||
| 26. Round | 14/01/2017 | Grimsby Town | - | Exeter City | 0:3 | ||||
| 27. Round | 21/01/2017 | Grimsby Town | - | Notts County | 2:0 | ||||
| 28. Round | 28/01/2017 | Stevenage FC | - | Grimsby Town | 2:0 | ||||
| 39. Round | 25/03/2017 | Accrington Stanley | - | Grimsby Town | 1:1 | ||||
| 40. Round | 01/04/2017 | Grimsby Town | - | Doncaster Rovers | 1:5 | ||||
| 41. Round | 08/04/2017 | Blackpool FC | - | Grimsby Town | 1:3 | ||||
| 42. Round | 14/04/2017 | Grimsby Town | - | Cambridge United | 2:1 | ||||
| 45. Round | 29/04/2017 | Barnet FC | - | Grimsby Town | 3:1 | ||||
| 46. Round | 06/05/2017 | Grimsby Town | - | Plymouth Argyle | 1:1 |
England