| 14. Round | 28/10/2008 | Leyton Orient | - | Milton Keynes Dons | 1:2 | ||||
| 20. Round | 12/12/2008 | Brighton & Hove Albion | - | Milton Keynes Dons | 2:4 | ||||
| 21. Round | 20/12/2008 | Milton Keynes Dons | - | Leeds United | 3:1 | ||||
| 22. Round | 26/12/2008 | Bristol Rovers | - | Milton Keynes Dons | 1:2 | ||||
| 23. Round | 28/12/2008 | Milton Keynes Dons | - | Southend United | 2:0 | ||||
| 25. Round | 12/01/2009 | Milton Keynes Dons | - | Colchester United | 1:1 |  |
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| 24. Round | 20/01/2009 | Peterborough United | - | Milton Keynes Dons | 0:0 | ||||
| 28. Round | 27/01/2009 | Milton Keynes Dons | - | Leyton Orient | 1:2 | ||||
| 31. Round | 24/03/2009 | Milton Keynes Dons | - | Crewe Alexandra | 2:2 | |
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| 41. Round | 04/04/2009 | Milton Keynes Dons | - | Brighton & Hove Albion | 2:0 | ||||
| 42. Round | 10/04/2009 | Southend United | - | Milton Keynes Dons | 0:2 | |
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| 43. Round | 13/04/2009 | Milton Keynes Dons | - | Bristol Rovers | 2:1 | ||||
| 44. Round | 18/04/2009 | Scunthorpe United | - | Milton Keynes Dons | 0:1 | ||||
| 45. Round | 25/04/2009 | Milton Keynes Dons | - | Walsall FC | 0:1 | ||||
| 46. Round | 02/05/2009 | Hereford United | - | Milton Keynes Dons | 0:1 |  |
England