| 28. Round | 14/01/2006 | Chester City | - | Boston United | 0:1 | ||||
| 24. Round | 18/01/2006 | Boston United | - | Carlisle United | 0:5 | ||||
| 29. Round | 21/01/2006 | Boston United | - | Bury FC | 3:1 |  |
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| 30. Round | 28/01/2006 | Rochdale AFC | - | Boston United | 1:1 | ||||
| 31. Round | 04/02/2006 | Boston United | - | Darlington FC | 0:0 | ||||
| 32. Round | 11/02/2006 | Grimsby Town | - | Boston United | 1:0 | ||||
| 34. Round | 18/02/2006 | Boston United | - | Wycombe Wanderers | 1:1 | ||||
| 37. Round | 11/03/2006 | Mansfield Town | - | Boston United | 5:0 | ||||
| 38. Round | 18/03/2006 | Boston United | - | Lincoln City | 2:1 | ||||
| 36. Round | 22/03/2006 | Boston United | - | Northampton Town | 0:1 | ||||
| 39. Round | 25/03/2006 | Carlisle United | - | Boston United | 4:2 | ||||
| 33. Round | 29/03/2006 | Boston United | - | Chester City | 1:3 | ||||
| 41. Round | 08/04/2006 | Leyton Orient | - | Boston United | 2:0 | ||||
| 44. Round | 22/04/2006 | Bristol Rovers | - | Boston United | 3:1 | ||||
| 45. Round | 29/04/2006 | Boston United | - | Rushden & Diamonds FC | 2:0 | ||||
| 46. Round | 06/05/2006 | Torquay United | - | Boston United | 0:0 |
England