| 1. Round | 09/08/2008 | Southend United | - | Peterborough United | 1:0 | ||||
| 2. Round | 16/08/2008 | Peterborough United | - | Leyton Orient | 3:0 | ||||
| 5. Round | 06/09/2008 | Peterborough United | - | Bristol Rovers | 5:4 | ||||
| 8. Round | 27/09/2008 | Milton Keynes Dons | - | Peterborough United | 1:2 | ||||
| 16. Round | 15/11/2008 | Yeovil Town | - | Peterborough United | 0:1 | ||||
| 18. Round | 25/11/2008 | Swindon Town | - | Peterborough United | 2:2 | ||||
| 21. Round | 20/12/2008 | Leicester City | - | Peterborough United | 4:0 | ||||
| 35. Round | 03/03/2009 | Leyton Orient | - | Peterborough United | 2:3 | ||||
| 36. Round | 07/03/2009 | Hartlepool United | - | Peterborough United | 1:2 | ||||
| 37. Round | 10/03/2009 | Peterborough United | - | Scunthorpe United | 2:1 | ||||
| 38. Round | 14/03/2009 | Peterborough United | - | Northampton Town | 1:0 | ||||
| 39. Round | 21/03/2009 | Bristol Rovers | - | Peterborough United | 0:1 | ||||
| 41. Round | 04/04/2009 | Oldham Athletic | - | Peterborough United | 1:2 | ||||
| 42. Round | 10/04/2009 | Peterborough United | - | Cheltenham Town | 1:1 | ||||
| 43. Round | 13/04/2009 | Millwall FC | - | Peterborough United | 2:0 | ||||
| 44. Round | 18/04/2009 | Peterborough United | - | Stockport County | 1:0 |
England