| 28. Round | 14/01/2006 | Leyton Orient | - | Northampton Town | 1:2 |  |
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| 29. Round | 21/01/2006 | Northampton Town | - | Macclesfield Town | 5:0 | ||||
| 24. Round | 24/01/2006 | Notts County | - | Northampton Town | 2:2 | ||||
| 37. Round | 10/03/2006 | Northampton Town | - | Carlisle United | 0:3 | ||||
| 38. Round | 18/03/2006 | Mansfield Town | - | Northampton Town | 1:0 | ||||
| 39. Round | 25/03/2006 | Northampton Town | - | Notts County | 2:0 |  |
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| 40. Round | 01/04/2006 | Peterborough United | - | Northampton Town | 0:1 | ||||
| 41. Round | 08/04/2006 | Northampton Town | - | Rochdale AFC | 2:2 | ||||
| 44. Round | 22/04/2006 | Oxford United | - | Northampton Town | 1:3 | ||||
| 45. Round | 29/04/2006 | Northampton Town | - | Chester City | 1:0 | ||||
| 46. Round | 06/05/2006 | Grimsby Town | - | Northampton Town | 1:1 | |
England