| 1. Round | 18/08/2012 | Exeter City | - | Morecambe FC | 0:3 |  |
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| 2. Round | 21/08/2012 | Morecambe FC | - | York City | 2:2 | ||||
| 5. Round | 08/09/2012 | Morecambe FC | - | Fleetwood Town | 0:4 | ||||
| 6. Round | 15/09/2012 | Aldershot Town | - | Morecambe FC | 0:0 | ||||
| 7. Round | 18/09/2012 | Bradford City | - | Morecambe FC | 3:1 | ||||
| 8. Round | 22/09/2012 | Morecambe FC | - | Plymouth Argyle | 2:3 | ||||
| 11. Round | 06/10/2012 | Morecambe FC | - | Burton Albion | 0:0 | ||||
| 14. Round | 23/10/2012 | Rotherham United | - | Morecambe FC | 2:1 | ||||
| 15. Round | 27/10/2012 | Torquay United | - | Morecambe FC | 1:0 | ||||
| 17. Round | 10/11/2012 | Morecambe FC | - | Barnet FC | 4:1 | ||||
| 18. Round | 17/11/2012 | Gillingham FC | - | Morecambe FC | 2:1 | ||||
| 19. Round | 20/11/2012 | Northampton Town | - | Morecambe FC | 3:0 | ||||
| 20. Round | 24/11/2012 | Morecambe FC | - | AFC Wimbledon | 3:1 | ||||
| 21. Round | 08/12/2012 | Wycombe Wanderers | - | Morecambe FC | 2:2 |  |
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| 24. Round | 26/12/2012 | Fleetwood Town | - | Morecambe FC | 1:0 | ||||
| 25. Round | 29/12/2012 | Chesterfield FC | - | Morecambe FC | 1:1 | ||||
| 26. Round | 01/01/2013 | Morecambe FC | - | Bradford City | 0:0 | ||||
| 28. Round | 12/01/2013 | Plymouth Argyle | - | Morecambe FC | 2:1 |
England