| Wednesday 3rd September 2008 | |||
| Northern First Round | |||
| Chesterfield | 2-2 | Grimsby Town | |
| (Grimsby Town won on penalties) | |||
| Tuesday 2nd September 2008 | |||
| Northern First Round | |||
| Crewe Alexandra | 3-0 | Macclesfield Town | |
| Hartlepool United | 0-3 | Leicester City | |
| Leeds United | 2-1 | Bradford City | |
| Oldham Athletic | 1-1 | Morecambe | |
| (Morecambe won on penalties) | |||
| Scunthorpe United | 2-1 | Notts County | |
| Stockport County | 1-0 | Port Vale | |
| Tranmere Rovers | 1-0 | Accrington Stanley | |
| Southern First Round | |||
| Aldershot Town | 2-2 | Swindon Town | |
| (Swindon Town won on penalties) | |||
| Bournemouth | 3-0 | Bristol Rovers | |
| Brentford | 2-2 | Yeovil Town | |
| (Brentford won on penalties) | |||
| Dagenham and Redb'ge | 4-2 | Barnet | |
| Exeter City | 1-2 | Shrewsbury Town | |
| Millwall | 0-1 | Colchester United | |
| Northampton Town | 0-1 | Brighton and Hove A | |
| Southend United | 2-4 | Leyton Orient | |