| 1 | Tue 4 Sep 2012 | 20-0 v Aldershot TownExeter City 0-0 Aldershot Town | Johnstone's Paint Trophy First Round |
| 2 | Tue 18 Sep 2012 | 23-2 v Wycombe WanderersExeter City 3-2 Wycombe Wanderers | npower League Two |
| 3 | Sat 22 Sep 2012 | 21-2 v Southend UnitedSouthend United 2-1 Exeter City | npower League Two |
| 4 | Tue 2 Oct 2012 | 22-1 v BarnetBarnet 1-2 Exeter City | npower League Two |
| 5 | Sat 6 Oct 2012 | 20-2 v Port ValeExeter City 0-2 Port Vale | npower League Two |
| 6 | Sat 20 Oct 2012 | 20-1 v ChesterfieldExeter City 0-1 Chesterfield | npower League Two |
| 7 | Tue 23 Oct 2012 | 21-1 v Dagenham & RedbridgeDagenham & Redbridge 1-1 Exeter City | npower League Two |
| 8 | Sat 27 Oct 2012 | 20-3 v Cheltenham TownCheltenham Town 3-0 Exeter City | npower League Two |
| 9 | Sat 3 Nov 2012 | 20-1 v BuryBury 1-0 Exeter City | FA Cup with Budweiser First Round |
| 10 | Tue 6 Nov 2012 | 22-0 v AFC WimbledonExeter City 2-0 AFC Wimbledon | npower League Two |
| 11 | Sat 10 Nov 2012 | 22-2 v Fleetwood TownExeter City 2-2 Fleetwood Town | npower League Two |
| 12 | Sat 17 Nov 2012 | 21-0 v Bradford CityBradford City 0-1 Exeter City | npower League Two |
| 13 | Tue 20 Nov 2012 | 23-2 v GillinghamGillingham 2-3 Exeter City | npower League Two |
| 14 | Sat 24 Nov 2012 | 20-1 v Rotherham UnitedExeter City 0-1 Rotherham United | npower League Two |
| 15 | Sat 8 Dec 2012 | 23-2 v RochdaleRochdale 2-3 Exeter City | npower League Two |
| 16 | Sat 15 Dec 2012 | 21-1 v Plymouth ArgyleExeter City 1-1 Plymouth Argyle | npower League Two |
| 17 | Wed 26 Dec 2012 | 21-3 v Oxford UnitedExeter City 1-3 Oxford United | npower League Two |
| 18 | Sat 29 Dec 2012 | 22-2 v BarnetExeter City 2-2 Barnet | npower League Two |
| 19 | Tue 1 Jan 2013 | 21-0 v Wycombe WanderersWycombe Wanderers 0-1 Exeter City | npower League Two |
| 20 | Sat 5 Jan 2013 | 22-1 v York CityYork City 1-2 Exeter City | npower League Two |
| 21 | Sat 12 Jan 2013 | 23-0 v Southend UnitedExeter City 3-0 Southend United | npower League Two |
| 22 | Tue 15 Jan 2013 | 21-1 v Torquay UnitedTorquay United 1-1 Exeter City | npower League Two |
| 23 | Mon 28 Jan 2013 | 20-1 v Torquay UnitedExeter City 0-1 Torquay United | npower League Two |
| 24 | Sat 9 Mar 2013 | 20-0 v Fleetwood TownFleetwood Town 0-0 Exeter City | npower League Two |
| 25 | Sat 16 Mar 2013 | 24-1 v Bradford CityExeter City 4-1 Bradford City | npower League Two |
| 26 | Mon 1 Apr 2013 | 21-2 v RochdaleExeter City 1-2 Rochdale | npower League Two |
| 27 | Sat 13 Apr 2013 | 22-2 v AFC WimbledonAFC Wimbledon 2-2 Exeter City | npower League Two |
| 28 | Sat 20 Apr 2013 | 20-1 v Cheltenham TownExeter City 0-1 Cheltenham Town | npower League Two |
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