| 32. Round | 09/02/2013 | Northampton Town | - | Rochdale AFC | 3:1 | ||||
| 33. Round | 16/02/2013 | Southend United | - | Northampton Town | 1:2 | ||||
| 24. Round | 19/02/2013 | AFC Wimbledon | - | Northampton Town | 1:1 |  |
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| 34. Round | 23/02/2013 | Northampton Town | - | Plymouth Argyle | 1:0 | ||||
| 35. Round | 26/02/2013 | Northampton Town | - | Bristol Rovers | 1:0 | ||||
| 36. Round | 02/03/2013 | Exeter City | - | Northampton Town | 3:0 | ||||
| 38. Round | 12/03/2013 | Morecambe FC | - | Northampton Town | 1:1 | ||||
| 40. Round | 23/03/2013 | Northampton Town | - | Oxford United | 1:0 | ||||
| 41. Round | 29/03/2013 | Northampton Town | - | Torquay United | 1:0 | ||||
| 42. Round | 01/04/2013 | Cheltenham Town | - | Northampton Town | 1:0 | ||||
| 43. Round | 06/04/2013 | Bradford City | - | Northampton Town | 1:0 | ||||
| 44. Round | 13/04/2013 | Northampton Town | - | York City | 0:2 | |
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| 39. Round | 16/04/2013 | Wycombe Wanderers | - | Northampton Town | 0:0 | ||||
| 45. Round | 20/04/2013 | Port Vale FC | - | Northampton Town | 2:2 | ||||
| 46. Round | 27/04/2013 | Northampton Town | - | Barnet FC | 2:0 |
England