| 1 | Sat 11 Aug 2012 | 22-2 v HydeBraintree Town 2-2 Hyde | Blue Square Bet Premier |
| 2 | Sat 18 Aug 2012 | 20-3 v AFC Telford UnitedAFC Telford United 3-0 Braintree Town | Blue Square Bet Premier |
| 3 | Sat 25 Aug 2012 | 21-2 v Newport CountyBraintree Town 1-2 Newport County | Blue Square Bet Premier |
| 4 | Tue 28 Aug 2012 | 24-1 v WokingWoking 1-4 Braintree Town | Blue Square Bet Premier |
| 5 | Sat 1 Sep 2012 | 22-1 v TamworthBraintree Town 2-1 Tamworth | Blue Square Bet Premier |
| 6 | Tue 4 Sep 2012 | 21-1 v Kidderminster HarriersBraintree Town 1-1 Kidderminster Harriers | Blue Square Bet Premier |
| 7 | Sat 8 Sep 2012 | 21-2 v Macclesfield TownMacclesfield Town 2-1 Braintree Town | Blue Square Bet Premier |
| 8 | Sat 15 Sep 2012 | 20-2 v Mansfield TownMansfield Town 2-0 Braintree Town | Blue Square Bet Premier |
| 9 | Sat 22 Sep 2012 | 20-0 v Stockport CountyBraintree Town 0-0 Stockport County | Blue Square Bet Premier |
| 10 | Tue 25 Sep 2012 | 20-2 v DartfordBraintree Town 0-2 Dartford | Blue Square Bet Premier |
| 11 | Sat 17 Nov 2012 | 20-3 v Grimsby TownGrimsby Town 3-0 Braintree Town | Blue Square Bet Premier |
| 12 | Sat 8 Dec 2012 | 22-0 v SouthportSouthport 0-2 Braintree Town | Blue Square Bet Premier |
| 13 | Tue 18 Dec 2012 | 23-1 v Forest Green RoversBraintree Town 3-1 Forest Green Rovers | Blue Square Bet Premier |
| 14 | Tue 1 Jan 2013 | 20-1 v Cambridge UnitedCambridge United 1-0 Braintree Town | Blue Square Bet Premier |
| 15 | Sat 5 Jan 2013 | 24-1 v TamworthTamworth 1-4 Braintree Town | Blue Square Bet Premier |
| 16 | Tue 8 Jan 2013 | 20-3 v Macclesfield TownBraintree Town 0-3 Macclesfield Town | Blue Square Bet Premier |
| 17 | Sat 12 Jan 2013 | 23-2 v AFC Telford UnitedBraintree Town 3-2 AFC Telford United | Blue Square Bet Premier |
| 18 | Sat 26 Jan 2013 | 24-2 v Nuneaton TownNuneaton Town 2-4 Braintree Town | Blue Square Bet Premier |
| 19 | Sat 9 Feb 2013 | 20-2 v Hereford UnitedBraintree Town 0-2 Hereford United | Blue Square Bet Premier |
| 20 | Tue 12 Feb 2013 | 21-4 v Forest Green RoversForest Green Rovers 4-1 Braintree Town | Blue Square Bet Premier |
| 21 | Tue 19 Feb 2013 | 22-0 v Grimsby TownBraintree Town 2-0 Grimsby Town | Blue Square Bet Premier |
| 22 | Tue 26 Feb 2013 | 22-0 v Luton TownBraintree Town 2-0 Luton Town | Blue Square Bet Premier |
| 23 | Sat 2 Mar 2013 | 22-1 v GatesheadGateshead 1-2 Braintree Town | Blue Square Bet Premier |
| 24 | Sat 16 Mar 2013 | 23-1 v Stockport CountyStockport County 1-3 Braintree Town | Blue Square Bet Premier |
| 25 | Tue 19 Mar 2013 | 21-1 v WokingBraintree Town 1-1 Woking | Blue Square Bet Premier |
| 26 | Thu 21 Mar 2013 | 22-2 v Nuneaton TownBraintree Town 2-2 Nuneaton Town | Blue Square Bet Premier |
| 27 | Wed 3 Apr 2013 | 21-3 v SouthportBraintree Town 1-3 Southport | Blue Square Bet Premier |
| 28 | Sat 6 Apr 2013 | 22-1 v HydeHyde 1-2 Braintree Town | Blue Square Bet Premier |
| 29 | Thu 11 Apr 2013 | 20-0 v DartfordDartford 0-0 Braintree Town | Blue Square Bet Premier |
| 30 | Tue 16 Apr 2013 | 21-1 v WrexhamWrexham 1-1 Braintree Town | Blue Square Bet Premier |
| 31 | Sat 20 Apr 2013 | 21-0 v BarrowBarrow 0-1 Braintree Town | Blue Square Bet Premier |
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