| 1 | Tue 25 Oct 2016 | 0-0 v Macclesfield TownMacclesfield Town 0-0 Chester | National League |
| 2 | Sat 29 Oct 2016 | 2-5 v Lincoln CityChester 2-5 Lincoln City | National League |
| 3 | Sat 12 Nov 2016 | 2-2 v Tranmere RoversTranmere Rovers 2-2 Chester | National League |
| 4 | Sat 19 Nov 2016 | 1-1 v BromleyChester 1-1 Bromley | National League |
| 5 | Tue 22 Nov 2016 | 2-2 v SouthportChester 2-2 Southport | National League |
| 6 | Sat 26 Nov 2016 | 3-0 v EastleighEastleigh 0-3 Chester | National League |
| 7 | Tue 29 Nov 2016 | 3-0 v North Ferriby UnitedChester 3-0 North Ferriby United | National League |
| 8 | Sat 3 Dec 2016 | 1-1 v GuiseleyGuiseley 1-1 Chester | National League |
| 9 | Sat 17 Dec 2016 | 2-0 v Aldershot TownChester 2-0 Aldershot Town | National League |
| 10 | Mon 26 Dec 2016 | 2-3 v Solihull MoorsSolihull Moors 3-2 Chester | National League |
| 11 | Sun 1 Jan 2017 | 0-3 v Solihull MoorsChester 0-3 Solihull Moors | National League |
| 12 | Sat 7 Jan 2017 | 12-1 v Braintree TownBraintree Town 1-2 Chester | National League |
| 13 | Sat 14 Jan 2017 | 10-2 v Forest Green RoversChester 0-2 Forest Green Rovers | FA Trophy Second Round |
| 14 | Sat 21 Jan 2017 | 11-1 v WrexhamChester 1-1 Wrexham | National League |
| 15 | Sat 18 Feb 2017 | 12-4 v Maidstone UnitedMaidstone United 4-2 Chester | National League |
| 16 | Sat 25 Feb 2017 | 11-0 v SouthportSouthport 0-1 Chester | National League |
| 17 | Fri 3 Mar 2017 | 12-3 v Tranmere RoversChester 2-3 Tranmere Rovers | National League |
| 18 | Sat 18 Mar 2017 | 10-1 v EastleighChester 0-1 Eastleigh | National League |
| 19 | Tue 21 Mar 2017 | 12-3 v Macclesfield TownChester 2-3 Macclesfield Town | National League |
| 20 | Sat 25 Mar 2017 | 11-0 v BromleyBromley 0-1 Chester | National League |
| 21 | Tue 28 Mar 2017 | 11-2 v BarrowChester 1-2 Barrow | National League |
| 22 | Sat 1 Apr 2017 | 11-0 v Torquay UnitedTorquay United 0-1 Chester | National League |
| 23 | Sat 8 Apr 2017 | 10-2 v York CityChester 0-2 York City | National League |
| 24 | Tue 11 Apr 2017 | 10-1 v Lincoln CityLincoln City 1-0 Chester | National League |
| 25 | Mon 17 Apr 2017 | 12-3 v WokingChester 2-3 Woking | National League |
| 26 | Sat 22 Apr 2017 | 12-5 v Sutton UnitedSutton United 5-2 Chester | National League |
| 27 | Sat 29 Apr 2017 | 10-2 v Boreham WoodChester 0-2 Boreham Wood | National League |
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