| Wednesday 3rd December 2008 | |||
| Second Round | |||
| Carlisle United | 0-2 | Crewe Alexandra | |
| Tuesday 2nd December 2008 | |||
| Second Round | |||
| Morecambe | 2-3 | Cheltenham Town | |
| Sunday 30th November 2008 | |||
| Second Round | |||
| Histon | 1-0 | Leeds United | |
| Notts County | 1-1 | Kettering Town | |
| Saturday 29th November 2008 | |||
| Second Round | |||
| Bournemouth | 0-0 | Blyth Spartans | |
| Bradford City | 1-2 | Leyton Orient | |
| Eastwood Town | 2-0 | Wycombe Wanderers | |
| Fleetwood Town | 2-3 | Hartlepool United | |
| Forest Green Rovers | 2-0 | Rochdale | |
| Gillingham | 0-0 | Stockport County | |
| Kidderminster Harr | 2-0 | Curzon Ashton | |
| Leicester City | 3-2 | Dagenham and Redb'ge | |
| Millwall | 3-0 | Aldershot Town | |
| Peterborough United | 0-0 | Tranmere Rovers | |
| Scunthorpe United | 4-0 | Alfreton Town | |
| Southend United | 3-1 | Luton Town | |
| Torquay United | 2-0 | Oxford United | |
| First Round Replay | |||
| Grays Athletic | 0-2 | Carlisle United | |
| Friday 28th November 2008 | |||
| Second Round | |||
| Barrow | 2-1 | Brentford | |
| Port Vale | 1-3 | Macclesfield Town | |
| Tuesday 9th December 2008 | |||
| Second Round | |||
| Chesterfield | v | Droylsden | 19:45 |
| Second Round Replay | |||
| Blyth Spartans | v | Bournemouth | |
| Stockport County | v | Gillingham | 19:45 |
| Tranmere Rovers | v | Peterborough United | 19:45 |
| Wednesday 10th December 2008 | |||
| Second Round Replay | |||
| Kettering Town | v | Notts County | 19:45 |
