| 1 | Sat 11 Aug 2012 | 32-2 v HydeBraintree Town 2-2 Hyde | Blue Square Bet Premier |
| 2 | Tue 14 Aug 2012 | 31-0 v Ebbsfleet UnitedEbbsfleet United 0-1 Braintree Town | Blue Square Bet Premier |
| 3 | Sat 18 Aug 2012 | 30-3 v AFC Telford UnitedAFC Telford United 3-0 Braintree Town | Blue Square Bet Premier |
| 4 | Sat 25 Aug 2012 | 31-2 v Newport CountyBraintree Town 1-2 Newport County | Blue Square Bet Premier |
| 5 | Tue 28 Aug 2012 | 34-1 v WokingWoking 1-4 Braintree Town | Blue Square Bet Premier |
| 6 | Sat 1 Sep 2012 | 32-1 v TamworthBraintree Town 2-1 Tamworth | Blue Square Bet Premier |
| 7 | Tue 4 Sep 2012 | 31-1 v Kidderminster HarriersBraintree Town 1-1 Kidderminster Harriers | Blue Square Bet Premier |
| 8 | Sat 8 Sep 2012 | 31-2 v Macclesfield TownMacclesfield Town 2-1 Braintree Town | Blue Square Bet Premier |
| 9 | Sat 29 Sep 2012 | 31-1 v Alfreton TownAlfreton Town 1-1 Braintree Town | Blue Square Bet Premier |
| 10 | Sat 6 Oct 2012 | 32-3 v BarrowBraintree Town 2-3 Barrow | Blue Square Bet Premier |
| 11 | Tue 9 Oct 2012 | 33-2 v Luton TownLuton Town 2-3 Braintree Town | Blue Square Bet Premier |
| 12 | Tue 6 Nov 2012 | 30-3 v Lincoln CityLincoln City 3-0 Braintree Town | Blue Square Bet Premier |
| 13 | Sat 10 Nov 2012 | 32-1 v GatesheadBraintree Town 2-1 Gateshead | Blue Square Bet Premier |
| 14 | Tue 13 Nov 2012 | 30-3 v Tranmere RoversBraintree Town 0-3 Tranmere Rovers | FA Cup with Budweiser First Round |
| 15 | Sat 17 Nov 2012 | 30-3 v Grimsby TownGrimsby Town 3-0 Braintree Town | Blue Square Bet Premier |
| 16 | Tue 20 Nov 2012 | 31-5 v WrexhamBraintree Town 1-5 Wrexham | Blue Square Bet Premier |
| 17 | Sat 8 Dec 2012 | 32-0 v SouthportSouthport 0-2 Braintree Town | Blue Square Bet Premier |
| 18 | Tue 18 Dec 2012 | 33-1 v Forest Green RoversBraintree Town 3-1 Forest Green Rovers | Blue Square Bet Premier |
| 19 | Wed 26 Dec 2012 | 30-3 v Cambridge UnitedBraintree Town 0-3 Cambridge United | Blue Square Bet Premier |
| 20 | Tue 1 Jan 2013 | 30-1 v Cambridge UnitedCambridge United 1-0 Braintree Town | Blue Square Bet Premier |
| 21 | Sat 12 Jan 2013 | 33-2 v AFC Telford UnitedBraintree Town 3-2 AFC Telford United | Blue Square Bet Premier |
| 22 | Sat 26 Jan 2013 | 34-2 v Nuneaton TownNuneaton Town 2-4 Braintree Town | Blue Square Bet Premier |
| 23 | Sat 9 Feb 2013 | 30-2 v Hereford UnitedBraintree Town 0-2 Hereford United | Blue Square Bet Premier |
| 24 | Tue 12 Feb 2013 | 31-4 v Forest Green RoversForest Green Rovers 4-1 Braintree Town | Blue Square Bet Premier |
| 25 | Tue 19 Feb 2013 | 32-0 v Grimsby TownBraintree Town 2-0 Grimsby Town | Blue Square Bet Premier |
| 26 | Tue 26 Feb 2013 | 32-0 v Luton TownBraintree Town 2-0 Luton Town | Blue Square Bet Premier |
| 27 | Sat 2 Mar 2013 | 32-1 v GatesheadGateshead 1-2 Braintree Town | Blue Square Bet Premier |
| 28 | Sat 16 Mar 2013 | 33-1 v Stockport CountyStockport County 1-3 Braintree Town | Blue Square Bet Premier |
| 29 | Tue 19 Mar 2013 | 31-1 v WokingBraintree Town 1-1 Woking | Blue Square Bet Premier |
| 30 | Thu 21 Mar 2013 | 32-2 v Nuneaton TownBraintree Town 2-2 Nuneaton Town | Blue Square Bet Premier |
| 31 | Tue 26 Mar 2013 | 30-3 v Lincoln CityBraintree Town 0-3 Lincoln City | Blue Square Bet Premier |
| 32 | Thu 28 Mar 2013 | 32-1 v Alfreton TownBraintree Town 2-1 Alfreton Town | Blue Square Bet Premier |
| 33 | Sat 30 Mar 2013 | 31-2 v Kidderminster HarriersKidderminster Harriers 2-1 Braintree Town | Blue Square Bet Premier |
| 34 | Wed 3 Apr 2013 | 31-3 v SouthportBraintree Town 1-3 Southport | Blue Square Bet Premier |
| 35 | Sat 6 Apr 2013 | 32-1 v HydeHyde 1-2 Braintree Town | Blue Square Bet Premier |
| 36 | Thu 11 Apr 2013 | 30-0 v DartfordDartford 0-0 Braintree Town | Blue Square Bet Premier |
| 37 | Sat 13 Apr 2013 | 32-1 v Mansfield TownBraintree Town 2-1 Mansfield Town | Blue Square Bet Premier |
| 38 | Tue 16 Apr 2013 | 31-1 v WrexhamWrexham 1-1 Braintree Town | Blue Square Bet Premier |
| 39 | Sat 20 Apr 2013 | 31-0 v BarrowBarrow 0-1 Braintree Town | Blue Square Bet Premier |
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