| 1 | Tue 4 Sep 2012 | 171-0 v Milton Keynes DonsNorthampton Town 1-0 Milton Keynes Dons | Johnstone's Paint Trophy First Round |
| 2 | Sat 10 Nov 2012 | 174-2 v Accrington StanleyAccrington Stanley 2-4 Northampton Town | npower League Two |
| 3 | Sat 17 Nov 2012 | 173-1 v Wycombe WanderersNorthampton Town 3-1 Wycombe Wanderers | npower League Two |
| 4 | Tue 20 Nov 2012 | 173-0 v MorecambeNorthampton Town 3-0 Morecambe | npower League Two |
| 5 | Sat 24 Nov 2012 | 171-2 v Oxford UnitedOxford United 2-1 Northampton Town | npower League Two |
| 6 | Wed 5 Dec 2012 | 170-3 v Leyton OrientNorthampton Town 0-3 Leyton Orient | Johnstone's Paint Trophy Southern Area Quarter Final |
| 7 | Sat 8 Dec 2012 | 172-3 v Cheltenham TownNorthampton Town 2-3 Cheltenham Town | npower League Two |
| 8 | Sat 15 Dec 2012 | 171-1 v Torquay UnitedTorquay United 1-1 Northampton Town | npower League Two |
| 9 | Sat 22 Dec 2012 | 172-0 v Aldershot TownNorthampton Town 2-0 Aldershot Town | npower League Two |
| 10 | Tue 1 Jan 2013 | 173-1 v Dagenham & RedbridgeNorthampton Town 3-1 Dagenham & Redbridge | npower League Two |
| 11 | Sat 5 Jan 2013 | 173-1 v Fleetwood TownNorthampton Town 3-1 Fleetwood Town | npower League Two |
| 12 | Sat 12 Jan 2013 | 170-3 v ChesterfieldChesterfield 3-0 Northampton Town | npower League Two |
| 13 | Sat 19 Jan 2013 | 171-0 v Burton AlbionNorthampton Town 1-0 Burton Albion | npower League Two |
| 14 | Tue 22 Jan 2013 | 172-1 v Aldershot TownAldershot Town 1-2 Northampton Town | npower League Two |
| 15 | Tue 29 Jan 2013 | 170-2 v GillinghamGillingham 2-0 Northampton Town | npower League Two |
| 16 | Sat 2 Feb 2013 | 171-3 v Rotherham UnitedRotherham United 3-1 Northampton Town | npower League Two |
| 17 | Sat 9 Feb 2013 | 173-1 v RochdaleNorthampton Town 3-1 Rochdale | npower League Two |
| 18 | Tue 19 Feb 2013 | 171-1 v AFC WimbledonAFC Wimbledon 1-1 Northampton Town | npower League Two |
| 19 | Sat 23 Feb 2013 | 171-0 v Plymouth ArgyleNorthampton Town 1-0 Plymouth Argyle | npower League Two |
| 20 | Tue 26 Feb 2013 | 171-0 v Bristol RoversNorthampton Town 1-0 Bristol Rovers | npower League Two |
| 21 | Sat 2 Mar 2013 | 170-3 v Exeter CityExeter City 3-0 Northampton Town | npower League Two |
| 22 | Sat 9 Mar 2013 | 172-0 v Accrington StanleyNorthampton Town 2-0 Accrington Stanley | npower League Two |
| 23 | Sat 23 Mar 2013 | 171-0 v Oxford UnitedNorthampton Town 1-0 Oxford United | npower League Two |
| 24 | Fri 29 Mar 2013 | 171-0 v Torquay UnitedNorthampton Town 1-0 Torquay United | npower League Two |
| 25 | Sat 6 Apr 2013 | 170-1 v Bradford CityBradford City 1-0 Northampton Town | npower League Two |
| 26 | Sat 13 Apr 2013 | 170-2 v York CityNorthampton Town 0-2 York City | npower League Two |
| 27 | Sat 27 Apr 2013 | 172-0 v BarnetNorthampton Town 2-0 Barnet | npower League Two |
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