| 1 | Sat 29 Oct 2016 | 2-2 v Sutton UnitedYork City 2-2 Sutton United | National League |
| 2 | Sat 19 Nov 2016 | 0-2 v Dagenham & RedbridgeYork City 0-2 Dagenham & Redbridge | National League |
| 3 | Tue 22 Nov 2016 | 1-4 v Lincoln CityYork City 1-4 Lincoln City | National League |
| 4 | Sat 26 Nov 2016 | 0-3 v BromleyBromley 3-0 York City | National League |
| 5 | Tue 29 Nov 2016 | 1-1 v GuiseleyYork City 1-1 Guiseley | National League |
| 6 | Sat 3 Dec 2016 | 0-1 v Tranmere RoversTranmere Rovers 1-0 York City | National League |
| 7 | Sat 17 Dec 2016 | 0-0 v Torquay UnitedYork City 0-0 Torquay United | National League |
| 8 | Mon 26 Dec 2016 | 1-0 v North Ferriby UnitedNorth Ferriby United 0-1 York City | National League |
| 9 | Sun 1 Jan 2017 | 0-1 v North Ferriby UnitedYork City 0-1 North Ferriby United | National League |
| 10 | Sat 7 Jan 2017 | 2-2 v Dover AthleticDover Athletic 2-2 York City | National League |
| 11 | Sat 21 Jan 2017 | 2-1 v BarrowYork City 2-1 Barrow | National League |
| 12 | Sat 28 Jan 2017 | 0-0 v Aldershot TownAldershot Town 0-0 York City | National League |
| 13 | Sat 4 Feb 2017 | 3-0 v Nuneaton TownNuneaton Town 0-3 York City | FA Trophy Third Round |
| 14 | Sat 11 Feb 2017 | 1-1 v Maidstone UnitedYork City 1-1 Maidstone United | National League |
| 15 | Sat 18 Feb 2017 | 1-1 v Boreham WoodBoreham Wood 1-1 York City | National League |
| 16 | Tue 21 Feb 2017 | 1-3 v GatesheadYork City 1-3 Gateshead | National League |
| 17 | Tue 28 Feb 2017 | 1-1 v Lincoln CityLincoln City 1-1 York City | National League |
| 18 | Sat 4 Mar 2017 | 3-1 v EastleighYork City 3-1 Eastleigh | National League |
| 19 | Sat 11 Mar 2017 | 2-2 v Sutton UnitedSutton United 2-2 York City | National League |
| 20 | Tue 14 Mar 2017 | 2-1 v Lincoln CityYork City 2-1 Lincoln City | FA Trophy Semi Final |
| 21 | Tue 21 Mar 2017 | 5-3 v SouthportYork City 5-3 Southport | National League |
| 22 | Sat 25 Mar 2017 | 0-1 v Dagenham & RedbridgeDagenham & Redbridge 1-0 York City | National League |
| 23 | Tue 28 Mar 2017 | 3-1 v Macclesfield TownMacclesfield Town 1-3 York City | National League |
| 24 | Sat 1 Apr 2017 | 3-0 v Braintree TownYork City 3-0 Braintree Town | National League |
| 25 | Tue 4 Apr 2017 | 0-2 v BromleyYork City 0-2 Bromley | National League |
| 26 | Sat 8 Apr 2017 | 2-0 v ChesterChester 0-2 York City | National League |
| 27 | Fri 14 Apr 2017 | 2-1 v Solihull MoorsSolihull Moors 1-2 York City | National League |
| 28 | Mon 17 Apr 2017 | 1-3 v WrexhamYork City 1-3 Wrexham | National League |
| 29 | Sat 22 Apr 2017 | 1-1 v WokingWoking 1-1 York City | National League |
| 30 | Sat 29 Apr 2017 | 2-2 v Forest Green RoversYork City 2-2 Forest Green Rovers | National League |
| 31 | Sun 21 May 2017 | 3-2 v Macclesfield TownMacclesfield Town 2-3 York City | FA Trophy Final |
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