| Johnstone's Paint Trophy Matches |
| |  | | | |
| 11 Nov 2008: Round 1
|
| Accrington | | vs. | | Lincoln City |
| Bournemouth | | vs. | | Chester |
| Bradford City | | vs. | | Mansfield Town |
| Bristol Rovers | | vs. | | Barnet |
| Bury | | vs. | | Hartlepool |
| Cheltenh. Town | | vs. | | Brentford |
| Chesterfield | | vs. | | Shrewsbury |
| Darlington | | vs. | | Peterborough |
| MK Dons | | vs. | | Rochdale |
| Macclesfield | | vs. | | Tranmere |
| Morecambe | | vs. | | Grimsby Town |
| Northampton | | vs. | | Hereford |
| Notts County | | vs. | | Dagenh. Redbr. |
| Rotherham | | vs. | | Crewe |
| Walsall | | vs. | | Stockp. County |
| Wycombe | | vs. | | Wrexham |
| | | | | |
| 9 Dec 2008: Round 2
|
| Huddersfield | | vs. | | Wrexham or Wycombe |
| Luton Town | | vs. | | Northampton or Hereford |
| Swansea City | | vs. | | Dagenh. Redbr. or Notts County |
| Yeovil | | vs. | | Tranmere or Macclesfield |
| Hartlepool or Bury | | vs. | | Barnsley |
| Grimsby Town or Morecambe | | vs. | | Nott. Forest |
| Lincoln City or Accrington | | vs. | | Carlisle United |
| Bradford City or Mansfield Town | | vs. | | Leyton Orient |
| Darlington or Peterborough | | vs. | | Doncaster |
| Cheltenh. Town or Brentford | | vs. | | Gillingham |
| MK Dons or Rochdale | | vs. | | Brighton |
| Chesterfield or Shrewsbury | | vs. | | Stoke City |
| Bournemouth or Chester | | vs. | | Port Vale |
| Walsall or Stockp. County | | vs. | | Millwall |
| Bristol Rovers or Barnet | | vs. | | Swindon Town |
| Crewe or Rotherham | | vs. | | Plymouth Argyle |
| | | | | |
| 20 Jan 2009: Round 3
|
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
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| 28 Jan 2009: Round 3
|
| [TBD] | | vs. | | [TBD] |
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| 17 Feb 2009: Quarter-Final
|
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
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| 17 Mar 2009: Semi-Final
|
| [TBD] | | vs. | | [TBD] |
| [TBD] | | vs. | | [TBD] |
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| 3 May 2009: Final
|
| [TBD] | | vs. | | [TBD] |