| 25. Round | 02/01/2017 | Northampton Town | - | Bradford City | 1:2 | ||||
| 26. Round | 07/01/2017 | Bristol Rovers | - | Northampton Town | 5:0 | ||||
| 28. Round | 21/01/2017 | Milton Keynes Dons | - | Northampton Town | 5:3 |  |
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| 29. Round | 28/01/2017 | Northampton Town | - | Coventry City | 3:0 | ||||
| 31. Round | 11/02/2017 | Northampton Town | - | Chesterfield FC | 3:1 | ||||
| 32. Round | 14/02/2017 | Northampton Town | - | Swindon Town | 2:1 | ||||
| 33. Round | 18/02/2017 | Southend United | - | Northampton Town | 2:2 | ||||
| 34. Round | 25/02/2017 | Fleetwood Town | - | Northampton Town | 3:0 | ||||
| 35. Round | 28/02/2017 | Northampton Town | - | Oldham Athletic | 1:2 | ||||
| 36. Round | 04/03/2017 | Northampton Town | - | Charlton Athletic | 2:1 | ||||
| 37. Round | 11/03/2017 | AFC Wimbledon | - | Northampton Town | 0:1 | ||||
| 40. Round | 25/03/2017 | Northampton Town | - | Oxford United | 0:0 |
Scotland