| 1 | Tue 21 Aug 2012 | 22-2 v MorecambeMorecambe 2-2 York City | npower League Two |
| 2 | Sat 25 Aug 2012 | 23-1 v BarnetBarnet 1-3 York City | npower League Two |
| 3 | Sat 1 Sep 2012 | 23-1 v Oxford UnitedYork City 3-1 Oxford United | npower League Two |
| 4 | Tue 4 Sep 2012 | 21-0 v Rotherham UnitedRotherham United 0-1 York City | Johnstone's Paint Trophy First Round |
| 5 | Sat 8 Sep 2012 | 22-2 v ChesterfieldYork City 2-2 Chesterfield | npower League Two |
| 6 | Sat 15 Sep 2012 | 21-1 v Exeter CityExeter City 1-1 York City | npower League Two |
| 7 | Wed 19 Sep 2012 | 21-3 v Burton AlbionBurton Albion 3-1 York City | npower League Two |
| 8 | Sat 22 Sep 2012 | 20-0 v Cheltenham TownYork City 0-0 Cheltenham Town | npower League Two |
| 9 | Sat 29 Sep 2012 | 22-0 v Aldershot TownAldershot Town 0-2 York City | npower League Two |
| 10 | Sat 27 Oct 2012 | 20-0 v Southend UnitedSouthend United 0-0 York City | npower League Two |
| 11 | Tue 6 Nov 2012 | 21-1 v Northampton TownYork City 1-1 Northampton Town | npower League Two |
| 12 | Sat 10 Nov 2012 | 20-3 v AFC WimbledonYork City 0-3 AFC Wimbledon | npower League Two |
| 13 | Mon 12 Nov 2012 | 23-4 v AFC WimbledonAFC Wimbledon 4-3 York City | FA Cup with Budweiser First Round Replay |
| 14 | Sat 17 Nov 2012 | 22-2 v Port ValePort Vale 2-2 York City | npower League Two |
| 15 | Sat 24 Nov 2012 | 20-2 v Torquay UnitedYork City 0-2 Torquay United | npower League Two |
| 16 | Sat 1 Dec 2012 | 23-2 v RochdaleRochdale 2-3 York City | npower League Two |
| 17 | Wed 26 Dec 2012 | 20-3 v ChesterfieldChesterfield 3-0 York City | npower League Two |
| 18 | Sat 29 Dec 2012 | 20-0 v Fleetwood TownFleetwood Town 0-0 York City | npower League Two |
| 19 | Tue 1 Jan 2013 | 23-0 v Burton AlbionYork City 3-0 Burton Albion | npower League Two |
| 20 | Sat 5 Jan 2013 | 21-2 v Exeter CityYork City 1-2 Exeter City | npower League Two |
| 21 | Sat 12 Jan 2013 | 21-1 v Cheltenham TownCheltenham Town 1-1 York City | npower League Two |
| 22 | Sat 19 Jan 2013 | 20-0 v Aldershot TownYork City 0-0 Aldershot Town | npower League Two |
| 23 | Sat 26 Jan 2013 | 21-1 v GillinghamGillingham 1-1 York City | npower League Two |
| 24 | Sat 23 Feb 2013 | 20-0 v Oxford UnitedOxford United 0-0 York City | npower League Two |
| 25 | Tue 26 Feb 2013 | 21-1 v Rotherham UnitedRotherham United 1-1 York City | npower League Two |
| 26 | Sat 2 Mar 2013 | 20-2 v Bradford CityYork City 0-2 Bradford City | npower League Two |
| 27 | Sat 30 Mar 2013 | 20-0 v Bristol RoversBristol Rovers 0-0 York City | npower League Two |
| 28 | Mon 1 Apr 2013 | 22-0 v Plymouth ArgyleYork City 2-0 Plymouth Argyle | npower League Two |
| 29 | Sat 6 Apr 2013 | 21-1 v Accrington StanleyYork City 1-1 Accrington Stanley | npower League Two |
| 30 | Sat 13 Apr 2013 | 22-0 v Northampton TownNorthampton Town 0-2 York City | npower League Two |
| 31 | Sat 20 Apr 2013 | 22-1 v Southend UnitedYork City 2-1 Southend United | npower League Two |
| 32 | Sat 27 Apr 2013 | 21-0 v Dagenham & RedbridgeDagenham & Redbridge 0-1 York City | npower League Two |
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