| 27. Round | 29/01/2013 | Yeovil Town | - | Milton Keynes Dons | 2:1 | ||||
| 31. Round | 02/02/2013 | Milton Keynes Dons | - | AFC Bournemouth | 0:3 | ||||
| 32. Round | 09/02/2013 | Oldham Athletic | - | Milton Keynes Dons | 3:1 | ||||
| 34. Round | 23/02/2013 | Carlisle United | - | Milton Keynes Dons | 1:1 | ||||
| 35. Round | 26/02/2013 | Portsmouth FC | - | Milton Keynes Dons | 1:1 | ||||
| 36. Round | 02/03/2013 | Milton Keynes Dons | - | Preston North End | 1:1 | ||||
| 30. Round | 05/03/2013 | Milton Keynes Dons | - | Doncaster Rovers | 3:0 | ||||
| 37. Round | 09/03/2013 | Sheffield United | - | Milton Keynes Dons | 0:0 | ||||
| 38. Round | 12/03/2013 | Milton Keynes Dons | - | Shrewsbury Town | 2:3 | ||||
| 39. Round | 16/03/2013 | Milton Keynes Dons | - | Tranmere Rovers | 3:0 | ||||
| 29. Round | 19/03/2013 | Crewe Alexandra | - | Milton Keynes Dons | 2:1 |  |
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| 42. Round | 01/04/2013 | Milton Keynes Dons | - | Brentford FC | 2:0 | ||||
| 33. Round | 09/04/2013 | Milton Keynes Dons | - | Swindon Town | 2:0 | ||||
| 44. Round | 13/04/2013 | Leyton Orient | - | Milton Keynes Dons | 2:0 | ||||
| 40. Round | 16/04/2013 | Colchester United | - | Milton Keynes Dons | 0:2 | ||||
| 45. Round | 20/04/2013 | Milton Keynes Dons | - | Scunthorpe United | 0:1 |
England