| 1 | Sat 6 Aug 2016 | 60-3 v GatesheadGateshead 3-0 Chester | National League |
| 2 | Tue 9 Aug 2016 | 63-0 v Dagenham & RedbridgeChester 3-0 Dagenham & Redbridge | National League |
| 3 | Sat 13 Aug 2016 | 61-3 v Maidstone UnitedChester 1-3 Maidstone United | National League |
| 4 | Tue 16 Aug 2016 | 62-3 v BarrowBarrow 3-2 Chester | National League |
| 5 | Sat 20 Aug 2016 | 61-1 v Boreham WoodBoreham Wood 1-1 Chester | National League |
| 6 | Sat 27 Aug 2016 | 64-0 v Sutton UnitedChester 4-0 Sutton United | National League |
| 7 | Mon 29 Aug 2016 | 61-3 v WokingWoking 3-1 Chester | National League |
| 8 | Sat 3 Sep 2016 | 61-2 v Forest Green RoversChester 1-2 Forest Green Rovers | National League |
| 9 | Sat 10 Sep 2016 | 60-0 v Aldershot TownAldershot Town 0-0 Chester | National League |
| 10 | Tue 13 Sep 2016 | 62-0 v GuiseleyChester 2-0 Guiseley | National League |
| 11 | Sat 17 Sep 2016 | 61-0 v Braintree TownChester 1-0 Braintree Town | National League |
| 12 | Sat 24 Sep 2016 | 60-0 v WrexhamWrexham 0-0 Chester | National League |
| 13 | Sat 1 Oct 2016 | 65-0 v Dover AthleticChester 5-0 Dover Athletic | National League |
| 14 | Tue 4 Oct 2016 | 61-0 v North Ferriby UnitedNorth Ferriby United 0-1 Chester | National League |
| 15 | Sat 8 Oct 2016 | 61-0 v Torquay UnitedChester 1-0 Torquay United | National League |
| 16 | Sat 22 Oct 2016 | 61-1 v York CityYork City 1-1 Chester | National League |
| 17 | Tue 25 Oct 2016 | 60-0 v Macclesfield TownMacclesfield Town 0-0 Chester | National League |
| 18 | Sat 29 Oct 2016 | 62-5 v Lincoln CityChester 2-5 Lincoln City | National League |
| 19 | Sat 12 Nov 2016 | 62-2 v Tranmere RoversTranmere Rovers 2-2 Chester | National League |
| 20 | Sat 19 Nov 2016 | 61-1 v BromleyChester 1-1 Bromley | National League |
| 21 | Tue 22 Nov 2016 | 62-2 v SouthportChester 2-2 Southport | National League |
| 22 | Sat 26 Nov 2016 | 63-0 v EastleighEastleigh 0-3 Chester | National League |
| 23 | Tue 29 Nov 2016 | 63-0 v North Ferriby UnitedChester 3-0 North Ferriby United | National League |
| 24 | Sat 3 Dec 2016 | 61-1 v GuiseleyGuiseley 1-1 Chester | National League |
| 25 | Sat 17 Dec 2016 | 62-0 v Aldershot TownChester 2-0 Aldershot Town | National League |
| 26 | Mon 26 Dec 2016 | 62-3 v Solihull MoorsSolihull Moors 3-2 Chester | National League |
| 27 | Sun 1 Jan 2017 | 60-3 v Solihull MoorsChester 0-3 Solihull Moors | National League |
| 28 | Sat 7 Jan 2017 | 62-1 v Braintree TownBraintree Town 1-2 Chester | National League |
| 29 | Sat 14 Jan 2017 | 60-2 v Forest Green RoversChester 0-2 Forest Green Rovers | FA Trophy Second Round |
| 30 | Sat 21 Jan 2017 | 61-1 v WrexhamChester 1-1 Wrexham | National League |
| 31 | Sat 28 Jan 2017 | 61-3 v Dover AthleticDover Athletic 3-1 Chester | National League |
| 32 | Sat 4 Feb 2017 | 62-3 v Dagenham & RedbridgeDagenham & Redbridge 3-2 Chester | National League |
| 33 | Sat 11 Feb 2017 | 61-2 v GatesheadChester 1-2 Gateshead | National League |
| 34 | Sat 18 Feb 2017 | 62-4 v Maidstone UnitedMaidstone United 4-2 Chester | National League |
| 35 | Sat 25 Feb 2017 | 61-0 v SouthportSouthport 0-1 Chester | National League |
| 36 | Fri 3 Mar 2017 | 62-3 v Tranmere RoversChester 2-3 Tranmere Rovers | National League |
| 37 | Sat 18 Mar 2017 | 60-1 v EastleighChester 0-1 Eastleigh | National League |
| 38 | Tue 21 Mar 2017 | 62-3 v Macclesfield TownChester 2-3 Macclesfield Town | National League |
| 39 | Sat 25 Mar 2017 | 61-0 v BromleyBromley 0-1 Chester | National League |
| 40 | Tue 28 Mar 2017 | 61-2 v BarrowChester 1-2 Barrow | National League |
| 41 | Sat 1 Apr 2017 | 61-0 v Torquay UnitedTorquay United 0-1 Chester | National League |
| 42 | Sat 8 Apr 2017 | 60-2 v York CityChester 0-2 York City | National League |
| 43 | Tue 11 Apr 2017 | 60-1 v Lincoln CityLincoln City 1-0 Chester | National League |
| 44 | Mon 17 Apr 2017 | 62-3 v WokingChester 2-3 Woking | National League |
| 45 | Sat 22 Apr 2017 | 62-5 v Sutton UnitedSutton United 5-2 Chester | National League |
| 46 | Sat 29 Apr 2017 | 60-2 v Boreham WoodChester 0-2 Boreham Wood | National League |
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