| 5. Round | 26/08/2006 | Boston United | - | Milton Keynes Dons | 0:1 | ||||
| 7. Round | 09/09/2006 | Boston United | - | Stockport County | 2:1 | ||||
| 8. Round | 12/09/2006 | Barnet FC | - | Boston United | 3:3 |  |
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| 10. Round | 23/09/2006 | Boston United | - | Rochdale AFC | 0:3 | ||||
| 11. Round | 27/09/2006 | Boston United | - | Lincoln City | 1:0 | ||||
| 12. Round | 30/09/2006 | Swindon Town | - | Boston United | 1:1 | ||||
| 13. Round | 07/10/2006 | Bristol Rovers | - | Boston United | 1:0 | ||||
| 15. Round | 21/10/2006 | Bury FC | - | Boston United | 2:1 | ||||
| 16. Round | 28/10/2006 | Boston United | - | Wycombe Wanderers | 0:1 | ||||
| 17. Round | 04/11/2006 | Boston United | - | Notts County | 3:3 | ||||
| 18. Round | 18/11/2006 | Macclesfield Town | - | Boston United | 2:3 | ||||
| 19. Round | 25/11/2006 | Boston United | - | Hereford United | 1:1 | |
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| 20. Round | 05/12/2006 | Chester City | - | Boston United | 3:1 |
Ireland