| 1 | Sat 6 Aug 2016 | 0-0 v North Ferriby UnitedNorth Ferriby United 0-0 Braintree Town | National League |
| 2 | Tue 9 Aug 2016 | 1-1 v EastleighBraintree Town 1-1 Eastleigh | National League |
| 3 | Sat 13 Aug 2016 | 31-3 v Macclesfield TownBraintree Town 1-3 Macclesfield Town | National League |
| 4 | Tue 16 Aug 2016 | 31-2 v Maidstone UnitedMaidstone United 2-1 Braintree Town | National League |
| 5 | Sat 20 Aug 2016 | 32-0 v Aldershot TownBraintree Town 2-0 Aldershot Town | National League |
| 6 | Sat 27 Aug 2016 | 31-2 v BarrowBarrow 2-1 Braintree Town | National League |
| 7 | Mon 29 Aug 2016 | 31-3 v Torquay UnitedBraintree Town 1-3 Torquay United | National League |
| 8 | Sat 3 Sep 2016 | 30-0 v GuiseleyGuiseley 0-0 Braintree Town | National League |
| 9 | Sat 10 Sep 2016 | 31-4 v GatesheadBraintree Town 1-4 Gateshead | National League |
| 10 | Tue 13 Sep 2016 | 32-1 v Sutton UnitedSutton United 1-2 Braintree Town | National League |
| 11 | Sat 17 Sep 2016 | 30-1 v ChesterChester 1-0 Braintree Town | National League |
| 12 | Sat 24 Sep 2016 | 30-1 v Forest Green RoversBraintree Town 0-1 Forest Green Rovers | National League |
| 13 | Sat 1 Oct 2016 | 30-3 v Lincoln CityLincoln City 3-0 Braintree Town | National League |
| 14 | Tue 4 Oct 2016 | 31-2 v Boreham WoodBraintree Town 1-2 Boreham Wood | National League |
| 15 | Sat 8 Oct 2016 | 31-1 v York CityBraintree Town 1-1 York City | National League |
| 16 | Sat 22 Oct 2016 | 31-6 v Dover AthleticDover Athletic 6-1 Braintree Town | National League |
| 17 | Tue 25 Oct 2016 | 33-2 v WokingWoking 2-3 Braintree Town | National League |
| 18 | Sat 29 Oct 2016 | 30-1 v Solihull MoorsBraintree Town 0-1 Solihull Moors | National League |
| 19 | Sat 5 Nov 2016 | 37-0 v Eastbourne BoroughBraintree Town 7-0 Eastbourne Borough | Emirates FA Cup First Round |
| 20 | Sat 12 Nov 2016 | 31-0 v WrexhamWrexham 0-1 Braintree Town | National League |
| 21 | Sat 19 Nov 2016 | 30-1 v Tranmere RoversBraintree Town 0-1 Tranmere Rovers | National League |
| 22 | Tue 22 Nov 2016 | 32-2 v BromleyBraintree Town 2-2 Bromley | National League |
| 23 | Sat 26 Nov 2016 | 35-4 v SouthportSouthport 4-5 Braintree Town | National League |
| 24 | Sun 4 Dec 2016 | 32-5 v MillwallMillwall 5-2 Braintree Town | Emirates FA Cup Second Round |
| 25 | Sat 17 Dec 2016 | 31-1 v GatesheadGateshead 1-1 Braintree Town | National League |
| 26 | Tue 20 Dec 2016 | 31-0 v Boreham WoodBoreham Wood 0-1 Braintree Town | National League |
| 27 | Mon 26 Dec 2016 | 33-2 v Dagenham & RedbridgeBraintree Town 3-2 Dagenham & Redbridge | National League |
| 28 | Mon 2 Jan 2017 | 30-3 v Dagenham & RedbridgeDagenham & Redbridge 3-0 Braintree Town | National League |
| 29 | Sat 7 Jan 2017 | 31-2 v ChesterBraintree Town 1-2 Chester | National League |
| 30 | Tue 10 Jan 2017 | 31-0 v Sutton UnitedBraintree Town 1-0 Sutton United | National League |
| 31 | Sat 21 Jan 2017 | 31-1 v Forest Green RoversForest Green Rovers 1-1 Braintree Town | National League |
| 32 | Sat 11 Feb 2017 | 31-0 v North Ferriby UnitedBraintree Town 1-0 North Ferriby United | National League |
| 33 | Tue 14 Feb 2017 | 32-0 v EastleighEastleigh 0-2 Braintree Town | National League |
| 34 | Sat 18 Feb 2017 | 30-2 v Macclesfield TownMacclesfield Town 2-0 Braintree Town | National League |
| 35 | Sat 25 Feb 2017 | 30-0 v Maidstone UnitedBraintree Town 0-0 Maidstone United | National League |
| 36 | Tue 28 Feb 2017 | 35-0 v BromleyBromley 0-5 Braintree Town | National League |
| 37 | Sat 4 Mar 2017 | 31-2 v WrexhamBraintree Town 1-2 Wrexham | National League |
| 38 | Tue 7 Mar 2017 | 30-4 v Lincoln CityBraintree Town 0-4 Lincoln City | National League |
| 39 | Sat 11 Mar 2017 | 33-3 v Solihull MoorsSolihull Moors 3-3 Braintree Town | National League |
| 40 | Sat 18 Mar 2017 | 32-0 v SouthportBraintree Town 2-0 Southport | National League |
| 41 | Tue 21 Mar 2017 | 31-3 v WokingBraintree Town 1-3 Woking | National League |
| 42 | Sat 25 Mar 2017 | 30-1 v Tranmere RoversTranmere Rovers 1-0 Braintree Town | National League |
| 43 | Sat 1 Apr 2017 | 30-3 v York CityYork City 3-0 Braintree Town | National League |
| 44 | Sat 8 Apr 2017 | 31-2 v Dover AthleticBraintree Town 1-2 Dover Athletic | National League |
| 45 | Fri 14 Apr 2017 | 32-0 v GuiseleyBraintree Town 2-0 Guiseley | National League |
| 46 | Mon 17 Apr 2017 | 31-3 v Torquay UnitedTorquay United 3-1 Braintree Town | National League |
| 47 | Sat 22 Apr 2017 | 30-2 v BarrowBraintree Town 0-2 Barrow | National League |
| 48 | Sat 29 Apr 2017 | 30-2 v Aldershot TownAldershot Town 2-0 Braintree Town | National League |
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