| 1 | Sat 18 Aug 2012 | 30-3 v MorecambeExeter City 0-3 Morecambe | npower League Two |
| 2 | Tue 21 Aug 2012 | 32-1 v Aldershot TownAldershot Town 1-2 Exeter City | npower League Two |
| 3 | Sat 25 Aug 2012 | 33-0 v Accrington StanleyAccrington Stanley 0-3 Exeter City | npower League Two |
| 4 | Sat 1 Sep 2012 | 33-0 v Burton AlbionExeter City 3-0 Burton Albion | npower League Two |
| 5 | Tue 4 Sep 2012 | 30-0 v Aldershot TownExeter City 0-0 Aldershot Town | Johnstone's Paint Trophy First Round |
| 6 | Sat 8 Sep 2012 | 34-2 v Oxford UnitedOxford United 2-4 Exeter City | npower League Two |
| 7 | Sat 15 Sep 2012 | 31-1 v York CityExeter City 1-1 York City | npower League Two |
| 8 | Tue 18 Sep 2012 | 33-2 v Wycombe WanderersExeter City 3-2 Wycombe Wanderers | npower League Two |
| 9 | Sat 22 Sep 2012 | 31-2 v Southend UnitedSouthend United 2-1 Exeter City | npower League Two |
| 10 | Sat 29 Sep 2012 | 31-2 v Bristol RoversExeter City 1-2 Bristol Rovers | npower League Two |
| 11 | Tue 2 Oct 2012 | 32-1 v BarnetBarnet 1-2 Exeter City | npower League Two |
| 12 | Sat 6 Oct 2012 | 30-2 v Port ValeExeter City 0-2 Port Vale | npower League Two |
| 13 | Tue 23 Oct 2012 | 31-1 v Dagenham & RedbridgeDagenham & Redbridge 1-1 Exeter City | npower League Two |
| 14 | Sat 27 Oct 2012 | 30-3 v Cheltenham TownCheltenham Town 3-0 Exeter City | npower League Two |
| 15 | Sat 3 Nov 2012 | 30-1 v BuryBury 1-0 Exeter City | FA Cup with Budweiser First Round |
| 16 | Tue 6 Nov 2012 | 32-0 v AFC WimbledonExeter City 2-0 AFC Wimbledon | npower League Two |
| 17 | Sat 10 Nov 2012 | 32-2 v Fleetwood TownExeter City 2-2 Fleetwood Town | npower League Two |
| 18 | Sat 17 Nov 2012 | 31-0 v Bradford CityBradford City 0-1 Exeter City | npower League Two |
| 19 | Tue 20 Nov 2012 | 33-2 v GillinghamGillingham 2-3 Exeter City | npower League Two |
| 20 | Sat 8 Dec 2012 | 33-2 v RochdaleRochdale 2-3 Exeter City | npower League Two |
| 21 | Sat 15 Dec 2012 | 31-1 v Plymouth ArgyleExeter City 1-1 Plymouth Argyle | npower League Two |
| 22 | Wed 26 Dec 2012 | 31-3 v Oxford UnitedExeter City 1-3 Oxford United | npower League Two |
| 23 | Sat 29 Dec 2012 | 32-2 v BarnetExeter City 2-2 Barnet | npower League Two |
| 24 | Tue 1 Jan 2013 | 31-0 v Wycombe WanderersWycombe Wanderers 0-1 Exeter City | npower League Two |
| 25 | Sat 5 Jan 2013 | 32-1 v York CityYork City 1-2 Exeter City | npower League Two |
| 26 | Sat 12 Jan 2013 | 33-0 v Southend UnitedExeter City 3-0 Southend United | npower League Two |
| 27 | Tue 15 Jan 2013 | 31-1 v Torquay UnitedTorquay United 1-1 Exeter City | npower League Two |
| 28 | Mon 28 Jan 2013 | 30-1 v Torquay UnitedExeter City 0-1 Torquay United | npower League Two |
| 29 | Sat 2 Feb 2013 | 30-0 v Aldershot TownExeter City 0-0 Aldershot Town | npower League Two |
| 30 | Sat 9 Feb 2013 | 33-0 v MorecambeMorecambe 0-3 Exeter City | npower League Two |
| 31 | Fri 15 Feb 2013 | 32-0 v Accrington StanleyExeter City 2-0 Accrington Stanley | npower League Two |
| 32 | Sat 23 Feb 2013 | 32-4 v Burton AlbionBurton Albion 4-2 Exeter City | npower League Two |
| 33 | Tue 26 Feb 2013 | 32-0 v Port ValePort Vale 0-2 Exeter City | npower League Two |
| 34 | Sat 2 Mar 2013 | 33-0 v Northampton TownExeter City 3-0 Northampton Town | npower League Two |
| 35 | Wed 6 Mar 2013 | 30-2 v Bristol RoversBristol Rovers 2-0 Exeter City | npower League Two |
| 36 | Sat 9 Mar 2013 | 30-0 v Fleetwood TownFleetwood Town 0-0 Exeter City | npower League Two |
| 37 | Tue 12 Mar 2013 | 30-0 v GillinghamExeter City 0-0 Gillingham | npower League Two |
| 38 | Sat 16 Mar 2013 | 34-1 v Bradford CityExeter City 4-1 Bradford City | npower League Two |
| 39 | Sat 30 Mar 2013 | 30-1 v Plymouth ArgylePlymouth Argyle 1-0 Exeter City | npower League Two |
| 40 | Mon 1 Apr 2013 | 31-2 v RochdaleExeter City 1-2 Rochdale | npower League Two |
| 41 | Sat 6 Apr 2013 | 30-1 v Dagenham & RedbridgeExeter City 0-1 Dagenham & Redbridge | npower League Two |
| 42 | Tue 9 Apr 2013 | 31-4 v Rotherham UnitedRotherham United 4-1 Exeter City | npower League Two |
| 43 | Sat 13 Apr 2013 | 32-2 v AFC WimbledonAFC Wimbledon 2-2 Exeter City | npower League Two |
| 44 | Sat 20 Apr 2013 | 30-1 v Cheltenham TownExeter City 0-1 Cheltenham Town | npower League Two |
| 45 | Sat 27 Apr 2013 | 30-4 v ChesterfieldChesterfield 4-0 Exeter City | npower League Two |
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