| 32. Round | 14/02/2009 | Scunthorpe United | - | Bristol Rovers | 0:2 | ||||
| 33. Round | 21/02/2009 | Swindon Town | - | Scunthorpe United | 4:2 |  |
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| 30. Round | 24/02/2009 | Southend United | - | Scunthorpe United | 2:0 | ||||
| 34. Round | 28/02/2009 | Leeds United | - | Scunthorpe United | 3:2 | ||||
| 35. Round | 03/03/2009 | Scunthorpe United | - | Walsall FC | 1:1 | ||||
| 36. Round | 07/03/2009 | Scunthorpe United | - | Stockport County | 2:1 |  |
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| 37. Round | 10/03/2009 | Peterborough United | - | Scunthorpe United | 2:1 | |
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| 38. Round | 14/03/2009 | Carlisle United | - | Scunthorpe United | 1:1 | ||||
| 25. Round | 17/03/2009 | Scunthorpe United | - | Hereford United | 3:0 | ||||
| 39. Round | 21/03/2009 | Scunthorpe United | - | Brighton & Hove Albion | 2:0 | ||||
| 40. Round | 28/03/2009 | Scunthorpe United | - | Colchester United | 3:0 | |
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| 42. Round | 10/04/2009 | Scunthorpe United | - | Huddersfield Town | 1:2 | |
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| 43. Round | 13/04/2009 | Hartlepool United | - | Scunthorpe United | 2:3 | ||||
| 44. Round | 18/04/2009 | Scunthorpe United | - | Milton Keynes Dons | 0:1 | ||||
| 45. Round | 24/04/2009 | Leicester City | - | Scunthorpe United | 2:2 | ||||
| 31. Round | 28/04/2009 | Scunthorpe United | - | Cheltenham Town | 3:0 | |
England