| 7. Round | 09/09/2006 | Grimsby Town | - | Walsall FC | 2:1 | ||||
| 8. Round | 12/09/2006 | Rochdale AFC | - | Grimsby Town | 1:0 | ||||
| 9. Round | 16/09/2006 | Chester City | - | Grimsby Town | 0:2 |  |
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| 10. Round | 23/09/2006 | Grimsby Town | - | Stockport County | 0:1 | |
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| 11. Round | 26/09/2006 | Grimsby Town | - | Hartlepool United | 1:4 | |
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| 12. Round | 29/09/2006 | Darlington FC | - | Grimsby Town | 2:2 |  |
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| 13. Round | 08/10/2006 | Grimsby Town | - | Hereford United | 2:1 | ||||
| 14. Round | 14/10/2006 | Swindon Town | - | Grimsby Town | 3:0 | |
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| 16. Round | 28/10/2006 | Peterborough United | - | Grimsby Town | 2:2 | ||||
| 17. Round | 04/11/2006 | Grimsby Town | - | Milton Keynes Dons | 1:3 | |
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| 18. Round | 18/11/2006 | Wycombe Wanderers | - | Grimsby Town | 1:1 | ||||
| 20. Round | 05/12/2006 | Barnet FC | - | Grimsby Town | 0:1 | ||||
| 21. Round | 09/12/2006 | Grimsby Town | - | Shrewsbury Town | 2:1 | |
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| 22. Round | 16/12/2006 | Lincoln City | - | Grimsby Town | 2:0 | ||||
| 23. Round | 22/12/2006 | Grimsby Town | - | Torquay United | 2:0 | ||||
| 25. Round | 30/12/2006 | Stockport County | - | Grimsby Town | 3:0 | ||||
| 27. Round | 09/01/2007 | Grimsby Town | - | Chester City | 0:2 |
England