| Tuesday 17th October 2006 | |||
| Northern First Round | |||
| Accrington Stanley | 1-1 | Carlisle United | |
| (Accrington Stanley won on penalties) | |||
| Bradford City | 1-2 | Scunthorpe United | |
| Bury | 0-2 | Tranmere Rovers | |
| Hartlepool United | 3-1 | Rotherham United | |
| Huddersfield Town | 1-2 | Doncaster Rovers | |
| Lincoln City | 0-0 | Grimsby Town | |
| (Grimsby Town won on penalties) | |||
| Macclesfield Town | 0-1 | Stockport County | |
| Wrexham | 1-1 | Rochdale | |
| (Rochdale won on penalties) | |||
| Southern First Round | |||
| Brighton and Hove A | 2-0 | Boston United | |
| Bristol Rovers | 1-0 | Torquay United | |
| Gillingham | 1-2 | Nottingham Forest | |
| Hereford United | 1-2 | Shrewsbury Town | |
| Northampton Town | 0-0 | Brentford | |
| (Brentford won on penalties) | |||
| Notts County | 0-1 | Barnet | |
| Walsall | 1-1 | Swansea City | |
| (Swansea City won on penalties) | |||
| Wycombe Wanderers | 1-0 | Swindon Town | |
» English Johnstone's Paint Trophy 2006-2007 : Results
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