5th April 2009
| Final | Scunthorpe United | 2-3 | Luton Town |
17th February 2009
| Northern Section Final 2nd Leg | Rotherham United | 0-1 | Scunthorpe United |
| Southern Section Final 2nd Leg | Luton Town | 1-1 | Brighton & Hove Albion |
20th January 2009
| Southern Section Final 1st Leg | Brighton & Hove Albion | 0-0 | Luton Town |
| Northern Section Final 1st Leg | Scunthorpe United | 2-0 | Rotherham United |
16th December 2008
| Southern Section Semi-Final | Shrewsbury Town | 0-0 | Brighton & Hove Albion |
| Southern Section Semi-Final | Luton Town | 1-0 | Colchester United |
| Northern Section Semi-Final | Rotherham United | 1-1 |
| Northern Section Semi-Final | Scunthorpe United | 2-1 |
12th November 2008
| Southern Section Quarter-Final | Brighton & Hove Albion | 2-0 | Swindon Town |
4th November 2008
| Southern Section Quarter-Final | AFC Bournemouth | 0-1 | Colchester United |
| Southern Section Quarter-Final | Shrewsbury Town | 5-0 | Dagenham & Redbridge |
| Northern Section Quarter-Final | Rotherham United | 2-0 | Leicester City |
| Northern Section Quarter-Final | 1-0 |
| Northern Section Quarter-Final | Scunthorpe United | 1-0 |
| Northern Section Quarter-Final | 1-0 | Morecambe |
| Southern Section Quarter-Final | Walsall | 0-1 | Luton Town |
8th October 2008
| Northern Section 2nd Round | Rotherham United | 4-2 | Leeds United |
7th October 2008
| Northern Section 2nd Round | 1-0 |
| Southern Section 2nd Round | Cheltenham Town | 1-2 | Walsall |
| Northern Section 2nd Round | 1-1 | Morecambe |
| Northern Section 2nd Round | 1-0 | Huddersfield Town |
| Southern Section 2nd Round | 0-1 | Colchester United |
| Southern Section 2nd Round | Luton Town | 2-2 | Brentford |
| Southern Section 2nd Round | Wycombe Wanderers | 0-7 | Shrewsbury Town |
| Southern Section 2nd Round | Peterborough United | 0-1 | Dagenham & Redbridge |
| Northern Section 2nd Round | 2-2 | Carlisle United |
| Northern Section 2nd Round | Scunthorpe United | 2-1 | Grimsby Town |
| Southern Section 2nd Round | Brighton & Hove Albion | 2-2 | Leyton Orient |
| Southern Section 2nd Round | 1-2 | Swindon Town |
| Southern Section 2nd Round | 0-1 | AFC Bournemouth |
6th October 2008
| Northern Section 2nd Round | 1-0 | Crewe Alexandra |
23rd September 2008
| Northern Section 2nd Round | Leicester City | 0-0 | Lincoln City |
3rd September 2008
| Northern Section 1st Round | Chesterfield | 2-2 | Grimsby Town |
2nd September 2008
| Northern Section 1st Round | Leeds United | 2-1 | Bradford City |
| Northern Section 1st Round | Hartlepool United | 0-3 | Leicester City |
| Northern Section 1st Round | Scunthorpe United | 2-1 | Notts. County |
| Southern Section 1st Round | Northampton Town | 0-1 | Brighton & Hove Albion |
| Southern Section 1st Round | Exeter City | 1-2 | Shrewsbury Town |
| Southern Section 1st Round | Dagenham & Redbridge | 4-2 | Barnet |
| Northern Section 1st Round | Crewe Alexandra | 3-0 | Macclesfield Town |
| Southern Section 1st Round | Brentford | 2-2 |
| Southern Section 1st Round | AFC Bournemouth | 3-0 | Bristol Rovers |
| Southern Section 1st Round | 2-4 | Leyton Orient |
| Southern Section 1st Round | Aldershot Town | 2-2 | Swindon Town |
| Northern Section 1st Round | 1-0 |
| Northern Section 1st Round | Oldham Athletic | 1-1 | Morecambe |
| Southern Section 1st Round | Millwall | 0-1 | Colchester United |
| Northern Section 1st Round | 1-0 | Port Vale |