| 1. Round | 09/08/2008 | Wycombe Wanderers | - | Morecambe FC | 1:1 | ||||
| 2. Round | 16/08/2008 | Morecambe FC | - | Rotherham United | 1:3 | ||||
| 3. Round | 23/08/2008 | Bury FC | - | Morecambe FC | 2:1 |  |
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| 4. Round | 30/08/2008 | Morecambe FC | - | Dagenham & Redbridge | 1:2 | ||||
| 5. Round | 06/09/2008 | Morecambe FC | - | Shrewsbury Town | 1:0 | ||||
| 26. Round | 17/01/2009 | Morecambe FC | - | Gillingham FC | 0:1 | ||||
| 27. Round | 24/01/2009 | Chesterfield FC | - | Morecambe FC | 1:2 | ||||
| 28. Round | 27/01/2009 | Accrington Stanley | - | Morecambe FC | 1:0 | ||||
| 24. Round | 10/02/2009 | Morecambe FC | - | Lincoln City | 1:1 | ||||
| 45. Round | 25/04/2009 | Exeter City | - | Morecambe FC | 2:2 | ||||
| 46. Round | 02/05/2009 | Morecambe FC | - | AFC Bournemouth | 0:4 |
England