| 31. Round | 03/02/2007 | Boston United | - | Grimsby Town | 0:6 | ||||
| 34. Round | 20/02/2007 | Peterborough United | - | Boston United | 1:1 |  |
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| 35. Round | 24/02/2007 | Boston United | - | Hartlepool United | 0:1 | ||||
| 36. Round | 03/03/2007 | Milton Keynes Dons | - | Boston United | 3:2 | ||||
| 37. Round | 10/03/2007 | Boston United | - | Bristol Rovers | 2:1 | ||||
| 38. Round | 17/03/2007 | Mansfield Town | - | Boston United | 1:2 | ||||
| 39. Round | 23/03/2007 | Wycombe Wanderers | - | Boston United | 0:0 | ||||
| 40. Round | 31/03/2007 | Boston United | - | Bury FC | 0:1 | ||||
| 41. Round | 07/04/2007 | Notts County | - | Boston United | 2:0 | ||||
| 42. Round | 09/04/2007 | Boston United | - | Macclesfield Town | 4:1 |
England