| 1 | Sat 6 Aug 2016 | 1-1 v Maidstone UnitedMaidstone United 1-1 York City | National League |
| 2 | Tue 9 Aug 2016 | 1-0 v Macclesfield TownYork City 1-0 Macclesfield Town | National League |
| 3 | Sat 13 Aug 2016 | 1-1 v Boreham WoodYork City 1-1 Boreham Wood | National League |
| 4 | Tue 16 Aug 2016 | 1-6 v GatesheadGateshead 6-1 York City | National League |
| 5 | Sat 20 Aug 2016 | 1-2 v Forest Green RoversForest Green Rovers 2-1 York City | National League |
| 6 | Mon 29 Aug 2016 | 1-2 v WrexhamWrexham 2-1 York City | National League |
| 7 | Sat 3 Sep 2016 | 4-0 v Solihull MoorsYork City 4-0 Solihull Moors | National League |
| 8 | Sat 10 Sep 2016 | 0-2 v Torquay UnitedTorquay United 2-0 York City | National League |
| 9 | Tue 13 Sep 2016 | 0-0 v Tranmere RoversYork City 0-0 Tranmere Rovers | National League |
| 10 | Sat 17 Sep 2016 | 0-1 v Dover AthleticYork City 0-1 Dover Athletic | National League |
| 11 | Sat 24 Sep 2016 | 0-2 v BarrowBarrow 2-0 York City | National League |
| 12 | Sat 1 Oct 2016 | 0-1 v Aldershot TownYork City 0-1 Aldershot Town | National League |
| 13 | Tue 4 Oct 2016 | 81-6 v GuiseleyGuiseley 6-1 York City | National League |
| 14 | Sat 8 Oct 2016 | 1-1 v Braintree TownBraintree Town 1-1 York City | National League |
| 15 | Sat 22 Oct 2016 | 1-1 v ChesterYork City 1-1 Chester | National League |
| 16 | Tue 25 Oct 2016 | 0-2 v SouthportSouthport 2-0 York City | National League |
| 17 | Sat 29 Oct 2016 | 2-2 v Sutton UnitedYork City 2-2 Sutton United | National League |
| 18 | Sat 12 Nov 2016 | 1-1 v EastleighEastleigh 1-1 York City | National League |
| 19 | Sat 19 Nov 2016 | 0-2 v Dagenham & RedbridgeYork City 0-2 Dagenham & Redbridge | National League |
| 20 | Tue 22 Nov 2016 | 1-4 v Lincoln CityYork City 1-4 Lincoln City | National League |
| 21 | Sat 26 Nov 2016 | 0-3 v BromleyBromley 3-0 York City | National League |
| 22 | Tue 29 Nov 2016 | 1-1 v GuiseleyYork City 1-1 Guiseley | National League |
| 23 | Sat 3 Dec 2016 | 0-1 v Tranmere RoversTranmere Rovers 1-0 York City | National League |
| 24 | Sat 17 Dec 2016 | 0-0 v Torquay UnitedYork City 0-0 Torquay United | National League |
| 25 | Mon 26 Dec 2016 | 1-0 v North Ferriby UnitedNorth Ferriby United 0-1 York City | National League |
| 26 | Sun 1 Jan 2017 | 0-1 v North Ferriby UnitedYork City 0-1 North Ferriby United | National League |
| 27 | Sat 7 Jan 2017 | 2-2 v Dover AthleticDover Athletic 2-2 York City | National League |
| 28 | Sat 21 Jan 2017 | 2-1 v BarrowYork City 2-1 Barrow | National League |
| 29 | Sat 28 Jan 2017 | 0-0 v Aldershot TownAldershot Town 0-0 York City | National League |
| 30 | Sat 4 Feb 2017 | 3-0 v Nuneaton TownNuneaton Town 0-3 York City | FA Trophy Third Round |
| 31 | Sat 11 Feb 2017 | 1-1 v Maidstone UnitedYork City 1-1 Maidstone United | National League |
| 32 | Sat 18 Feb 2017 | 1-1 v Boreham WoodBoreham Wood 1-1 York City | National League |
| 33 | Tue 21 Feb 2017 | 1-3 v GatesheadYork City 1-3 Gateshead | National League |
| 34 | Tue 28 Feb 2017 | 1-1 v Lincoln CityLincoln City 1-1 York City | National League |
| 35 | Sat 4 Mar 2017 | 3-1 v EastleighYork City 3-1 Eastleigh | National League |
| 36 | Sat 11 Mar 2017 | 2-2 v Sutton UnitedSutton United 2-2 York City | National League |
| 37 | Tue 14 Mar 2017 | 2-1 v Lincoln CityYork City 2-1 Lincoln City | FA Trophy Semi Final |
| 38 | Tue 21 Mar 2017 | 5-3 v SouthportYork City 5-3 Southport | National League |
| 39 | Sat 25 Mar 2017 | 0-1 v Dagenham & RedbridgeDagenham & Redbridge 1-0 York City | National League |
| 40 | Tue 28 Mar 2017 | 3-1 v Macclesfield TownMacclesfield Town 1-3 York City | National League |
| 41 | Tue 4 Apr 2017 | 0-2 v BromleyYork City 0-2 Bromley | National League |
| 42 | Sat 8 Apr 2017 | 2-0 v ChesterChester 0-2 York City | National League |
| 43 | Fri 14 Apr 2017 | 2-1 v Solihull MoorsSolihull Moors 1-2 York City | National League |
| 44 | Mon 17 Apr 2017 | 1-3 v WrexhamYork City 1-3 Wrexham | National League |
| 45 | Sat 22 Apr 2017 | 1-1 v WokingWoking 1-1 York City | National League |
| 46 | Sat 29 Apr 2017 | 2-2 v Forest Green RoversYork City 2-2 Forest Green Rovers | National League |
| 47 | Sun 21 May 2017 | 3-2 v Macclesfield TownMacclesfield Town 2-3 York City | FA Trophy Final |
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