| 1 | Tue 28 Aug 2012 | 204-1 v WokingWoking 1-4 Braintree Town | Blue Square Bet Premier |
| 2 | Sat 1 Sep 2012 | 202-1 v TamworthBraintree Town 2-1 Tamworth | Blue Square Bet Premier |
| 3 | Tue 4 Sep 2012 | 201-1 v Kidderminster HarriersBraintree Town 1-1 Kidderminster Harriers | Blue Square Bet Premier |
| 4 | Sat 8 Sep 2012 | 201-2 v Macclesfield TownMacclesfield Town 2-1 Braintree Town | Blue Square Bet Premier |
| 5 | Sat 15 Sep 2012 | 200-2 v Mansfield TownMansfield Town 2-0 Braintree Town | Blue Square Bet Premier |
| 6 | Sat 22 Sep 2012 | 200-0 v Stockport CountyBraintree Town 0-0 Stockport County | Blue Square Bet Premier |
| 7 | Tue 25 Sep 2012 | 200-2 v DartfordBraintree Town 0-2 Dartford | Blue Square Bet Premier |
| 8 | Sat 29 Sep 2012 | 201-1 v Alfreton TownAlfreton Town 1-1 Braintree Town | Blue Square Bet Premier |
| 9 | Sat 6 Oct 2012 | 202-3 v BarrowBraintree Town 2-3 Barrow | Blue Square Bet Premier |
| 10 | Tue 9 Oct 2012 | 203-2 v Luton TownLuton Town 2-3 Braintree Town | Blue Square Bet Premier |
| 11 | Tue 6 Nov 2012 | 200-3 v Lincoln CityLincoln City 3-0 Braintree Town | Blue Square Bet Premier |
| 12 | Sat 10 Nov 2012 | 202-1 v GatesheadBraintree Town 2-1 Gateshead | Blue Square Bet Premier |
| 13 | Tue 13 Nov 2012 | 200-3 v Tranmere RoversBraintree Town 0-3 Tranmere Rovers | FA Cup with Budweiser First Round |
| 14 | Sat 17 Nov 2012 | 200-3 v Grimsby TownGrimsby Town 3-0 Braintree Town | Blue Square Bet Premier |
| 15 | Tue 20 Nov 2012 | 201-5 v WrexhamBraintree Town 1-5 Wrexham | Blue Square Bet Premier |
| 16 | Sat 8 Dec 2012 | 202-0 v SouthportSouthport 0-2 Braintree Town | Blue Square Bet Premier |
| 17 | Tue 18 Dec 2012 | 203-1 v Forest Green RoversBraintree Town 3-1 Forest Green Rovers | Blue Square Bet Premier |
| 18 | Wed 26 Dec 2012 | 200-3 v Cambridge UnitedBraintree Town 0-3 Cambridge United | Blue Square Bet Premier |
| 19 | Tue 1 Jan 2013 | 200-1 v Cambridge UnitedCambridge United 1-0 Braintree Town | Blue Square Bet Premier |
| 20 | Sat 5 Jan 2013 | 204-1 v TamworthTamworth 1-4 Braintree Town | Blue Square Bet Premier |
| 21 | Tue 8 Jan 2013 | 200-3 v Macclesfield TownBraintree Town 0-3 Macclesfield Town | Blue Square Bet Premier |
| 22 | Sat 12 Jan 2013 | 203-2 v AFC Telford UnitedBraintree Town 3-2 AFC Telford United | Blue Square Bet Premier |
| 23 | Sat 26 Jan 2013 | 204-2 v Nuneaton TownNuneaton Town 2-4 Braintree Town | Blue Square Bet Premier |
| 24 | Sat 9 Feb 2013 | 200-2 v Hereford UnitedBraintree Town 0-2 Hereford United | Blue Square Bet Premier |
| 25 | Tue 12 Feb 2013 | 201-4 v Forest Green RoversForest Green Rovers 4-1 Braintree Town | Blue Square Bet Premier |
| 26 | Tue 19 Feb 2013 | 202-0 v Grimsby TownBraintree Town 2-0 Grimsby Town | Blue Square Bet Premier |
| 27 | Tue 26 Feb 2013 | 202-0 v Luton TownBraintree Town 2-0 Luton Town | Blue Square Bet Premier |
| 28 | Sat 2 Mar 2013 | 202-1 v GatesheadGateshead 1-2 Braintree Town | Blue Square Bet Premier |
| 29 | Sat 16 Mar 2013 | 203-1 v Stockport CountyStockport County 1-3 Braintree Town | Blue Square Bet Premier |
| 30 | Tue 19 Mar 2013 | 201-1 v WokingBraintree Town 1-1 Woking | Blue Square Bet Premier |
| 31 | Thu 21 Mar 2013 | 202-2 v Nuneaton TownBraintree Town 2-2 Nuneaton Town | Blue Square Bet Premier |
| 32 | Sat 13 Apr 2013 | 202-1 v Mansfield TownBraintree Town 2-1 Mansfield Town | Blue Square Bet Premier |
| 33 | Tue 16 Apr 2013 | 201-1 v WrexhamWrexham 1-1 Braintree Town | Blue Square Bet Premier |
| 34 | Sat 20 Apr 2013 | 201-0 v BarrowBarrow 0-1 Braintree Town | Blue Square Bet Premier |
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