| 1 | Sat 3 Aug 2013 | 31-0 v Northampton TownYork City 1-0 Northampton Town | Sky Bet League Two |
| 2 | Sat 10 Aug 2013 | 30-2 v Dagenham & RedbridgeDagenham & Redbridge 2-0 York City | Sky Bet League Two |
| 3 | Sat 17 Aug 2013 | 30-0 v Hartlepool UnitedYork City 0-0 Hartlepool United | Sky Bet League Two |
| 4 | Sat 24 Aug 2013 | 32-3 v Bristol RoversBristol Rovers 3-2 York City | Sky Bet League Two |
| 5 | Sat 31 Aug 2013 | 31-2 v Exeter CityExeter City 2-1 York City | Sky Bet League Two |
| 6 | Sat 7 Sep 2013 | 30-2 v AFC WimbledonYork City 0-2 AFC Wimbledon | Sky Bet League Two |
| 7 | Sat 14 Sep 2013 | 31-2 v Mansfield TownYork City 1-2 Mansfield Town | Sky Bet League Two |
| 8 | Sat 21 Sep 2013 | 31-1 v Wycombe WanderersWycombe Wanderers 1-1 York City | Sky Bet League Two |
| 9 | Sat 28 Sep 2013 | 34-2 v PortsmouthYork City 4-2 Portsmouth | Sky Bet League Two |
| 10 | Sat 5 Oct 2013 | 33-0 v Torquay UnitedTorquay United 0-3 York City | Sky Bet League Two |
| 11 | Tue 8 Oct 2013 | 30-3 v Rotherham UnitedYork City 0-3 Rotherham United | Johnstone's Paint Trophy Northern Area Second Round |
| 12 | Tue 22 Oct 2013 | 32-2 v ChesterfieldChesterfield 2-2 York City | Sky Bet League Two |
| 13 | Sat 26 Oct 2013 | 30-2 v Fleetwood TownYork City 0-2 Fleetwood Town | Sky Bet League Two |
| 14 | Tue 29 Oct 2013 | 34-1 v Scunthorpe UnitedYork City 4-1 Scunthorpe United | Sky Bet League Two |
| 15 | Sat 2 Nov 2013 | 32-2 v Cheltenham TownCheltenham Town 2-2 York City | Sky Bet League Two |
| 16 | Sat 16 Nov 2013 | 31-1 v Plymouth ArgyleYork City 1-1 Plymouth Argyle | Sky Bet League Two |
| 17 | Sat 23 Nov 2013 | 31-2 v Southend UnitedSouthend United 2-1 York City | Sky Bet League Two |
| 18 | Tue 26 Nov 2013 | 30-0 v MorecambeMorecambe 0-0 York City | Sky Bet League Two |
| 19 | Sat 30 Nov 2013 | 30-0 v RochdaleYork City 0-0 Rochdale | Sky Bet League Two |
| 20 | Sat 14 Dec 2013 | 31-1 v Burton AlbionBurton Albion 1-1 York City | Sky Bet League Two |
| 21 | Sat 21 Dec 2013 | 30-0 v Oxford UnitedYork City 0-0 Oxford United | Sky Bet League Two |
| 22 | Thu 26 Dec 2013 | 31-1 v Accrington StanleyAccrington Stanley 1-1 York City | Sky Bet League Two |
| 23 | Sun 29 Dec 2013 | 31-2 v BuryBury 2-1 York City | Sky Bet League Two |
| 24 | Wed 1 Jan 2014 | 31-0 v MorecambeYork City 1-0 Morecambe | Sky Bet League Two |
| 25 | Sat 4 Jan 2014 | 33-1 v Dagenham & RedbridgeYork City 3-1 Dagenham & Redbridge | Sky Bet League Two |
| 26 | Sat 11 Jan 2014 | 32-0 v Northampton TownNorthampton Town 0-2 York City | Sky Bet League Two |
| 27 | Sat 18 Jan 2014 | 30-0 v Bristol RoversYork City 0-0 Bristol Rovers | Sky Bet League Two |
| 28 | Sat 25 Jan 2014 | 30-2 v Hartlepool UnitedHartlepool United 2-0 York City | Sky Bet League Two |
| 29 | Tue 28 Jan 2014 | 30-2 v ChesterfieldYork City 0-2 Chesterfield | Sky Bet League Two |
| 30 | Sat 1 Feb 2014 | 32-1 v Fleetwood TownFleetwood Town 1-2 York City | Sky Bet League Two |
| 31 | Sat 8 Feb 2014 | 30-0 v Cheltenham TownYork City 0-0 Cheltenham Town | Sky Bet League Two |
| 32 | Sat 15 Feb 2014 | 34-0 v Plymouth ArgylePlymouth Argyle 0-4 York City | Sky Bet League Two |
| 33 | Sat 22 Feb 2014 | 30-0 v Southend UnitedYork City 0-0 Southend United | Sky Bet League Two |
| 34 | Sat 1 Mar 2014 | 32-1 v Exeter CityYork City 2-1 Exeter City | Sky Bet League Two |
| 35 | Sat 8 Mar 2014 | 31-0 v AFC WimbledonAFC Wimbledon 0-1 York City | Sky Bet League Two |
| 36 | Tue 11 Mar 2014 | 31-0 v Mansfield TownMansfield Town 0-1 York City | Sky Bet League Two |
| 37 | Sat 15 Mar 2014 | 32-0 v Wycombe WanderersYork City 2-0 Wycombe Wanderers | Sky Bet League Two |
| 38 | Sat 22 Mar 2014 | 31-0 v PortsmouthPortsmouth 0-1 York City | Sky Bet League Two |
| 39 | Tue 25 Mar 2014 | 31-0 v Torquay UnitedYork City 1-0 Torquay United | Sky Bet League Two |
| 40 | Sat 29 Mar 2014 | 30-0 v Burton AlbionYork City 0-0 Burton Albion | Sky Bet League Two |
| 41 | Sat 12 Apr 2014 | 31-1 v Accrington StanleyYork City 1-1 Accrington Stanley | Sky Bet League Two |
| 42 | Fri 18 Apr 2014 | 31-0 v Oxford UnitedOxford United 0-1 York City | Sky Bet League Two |
| 43 | Mon 21 Apr 2014 | 31-0 v BuryYork City 1-0 Bury | Sky Bet League Two |
| 44 | Sat 26 Apr 2014 | 31-0 v Newport CountyYork City 1-0 Newport County | Sky Bet League Two |
| 45 | Sat 3 May 2014 | 32-2 v Scunthorpe UnitedScunthorpe United 2-2 York City | Sky Bet League Two |
| 46 | Mon 12 May 2014 | 30-1 v Fleetwood TownYork City 0-1 Fleetwood Town | Sky Bet League Two Play-off Semi Final |
| 47 | Fri 16 May 2014 | 30-0 v Fleetwood TownFleetwood Town 0-0 York City | Sky Bet League Two Play-off Semi Final |
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