| 4. Round | 30/08/2008 | Tranmere Rovers | - | Northampton Town | 4:1 | ||||
| 6. Round | 13/09/2008 | Northampton Town | - | Peterborough United | 1:1 | ||||
| 5. Round | 16/09/2008 | Stockport County | - | Northampton Town | 1:1 | ||||
| 7. Round | 20/09/2008 | Huddersfield Town | - | Northampton Town | 3:2 | ||||
| 12. Round | 21/10/2008 | Swindon Town | - | Northampton Town | 2:1 | ||||
| 15. Round | 01/11/2008 | Walsall FC | - | Northampton Town | 3:1 | ||||
| 16. Round | 15/11/2008 | Northampton Town | - | Oldham Athletic | 0:1 | ||||
| 17. Round | 22/11/2008 | Hereford United | - | Northampton Town | 0:2 | ||||
| 25. Round | 10/01/2009 | Northampton Town | - | Huddersfield Town | 1:1 | ||||
| 26. Round | 16/01/2009 | Hartlepool United | - | Northampton Town | 2:0 | ||||
| 29. Round | 31/01/2009 | Northampton Town | - | Leicester City | 1:2 | ||||
| 32. Round | 14/02/2009 | Oldham Athletic | - | Northampton Town | 2:1 | ||||
| 35. Round | 28/04/2009 | Northampton Town | - | Milton Keynes Dons | 0:1 | ||||
| 46. Round | 02/05/2009 | Leeds United | - | Northampton Town | 3:0 |  |
England