| 2. Round | 10/08/2005 | Boston United | - | Shrewsbury Town | 1:1 |  |
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| 3. Round | 13/08/2005 | Boston United | - | Stockport County | 2:2 | |
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| 4. Round | 20/08/2005 | Cheltenham Town | - | Boston United | 3:0 | ||||
| 5. Round | 27/08/2005 | Boston United | - | Mansfield Town | 2:2 | ||||
| 6. Round | 29/08/2005 | Northampton Town | - | Boston United | 3:2 | ||||
| 7. Round | 04/09/2005 | Macclesfield Town | - | Boston United | 2:2 | |
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| 8. Round | 10/09/2005 | Boston United | - | Rochdale AFC | 3:2 | ||||
| 9. Round | 17/09/2005 | Bury FC | - | Boston United | 1:1 | ||||
| 10. Round | 24/09/2005 | Boston United | - | Grimsby Town | 1:1 | ||||
| 14. Round | 15/10/2005 | Boston United | - | Bristol Rovers | 3:1 | ||||
| 15. Round | 22/10/2005 | Oxford United | - | Boston United | 0:0 | ||||
| 16. Round | 29/10/2005 | Boston United | - | Torquay United | 2:0 | ||||
| 17. Round | 11/11/2005 | Rushden & Diamonds FC | - | Boston United | 1:0 | ||||
| 18. Round | 19/11/2005 | Boston United | - | Notts County | 1:2 | |
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| 19. Round | 26/11/2005 | Boston United | - | Wrexham AFC | 2:1 | ||||
| 25. Round | 31/12/2005 | Barnet FC | - | Boston United | 1:0 | |
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| 26. Round | 02/01/2006 | Boston United | - | Leyton Orient | 1:2 |
England