| 1 | Tue 25 Sep 2012 | 140-2 v DartfordBraintree Town 0-2 Dartford | Blue Square Bet Premier |
| 2 | Sat 29 Sep 2012 | 141-1 v Alfreton TownAlfreton Town 1-1 Braintree Town | Blue Square Bet Premier |
| 3 | Tue 9 Oct 2012 | 143-2 v Luton TownLuton Town 2-3 Braintree Town | Blue Square Bet Premier |
| 4 | Tue 6 Nov 2012 | 140-3 v Lincoln CityLincoln City 3-0 Braintree Town | Blue Square Bet Premier |
| 5 | Sat 10 Nov 2012 | 142-1 v GatesheadBraintree Town 2-1 Gateshead | Blue Square Bet Premier |
| 6 | Tue 13 Nov 2012 | 140-3 v Tranmere RoversBraintree Town 0-3 Tranmere Rovers | FA Cup with Budweiser First Round |
| 7 | Sat 17 Nov 2012 | 140-3 v Grimsby TownGrimsby Town 3-0 Braintree Town | Blue Square Bet Premier |
| 8 | Tue 20 Nov 2012 | 141-5 v WrexhamBraintree Town 1-5 Wrexham | Blue Square Bet Premier |
| 9 | Tue 18 Dec 2012 | 143-1 v Forest Green RoversBraintree Town 3-1 Forest Green Rovers | Blue Square Bet Premier |
| 10 | Wed 26 Dec 2012 | 140-3 v Cambridge UnitedBraintree Town 0-3 Cambridge United | Blue Square Bet Premier |
| 11 | Sat 5 Jan 2013 | 144-1 v TamworthTamworth 1-4 Braintree Town | Blue Square Bet Premier |
| 12 | Tue 8 Jan 2013 | 140-3 v Macclesfield TownBraintree Town 0-3 Macclesfield Town | Blue Square Bet Premier |
| 13 | Tue 26 Mar 2013 | 140-3 v Lincoln CityBraintree Town 0-3 Lincoln City | Blue Square Bet Premier |
| 14 | Thu 28 Mar 2013 | 142-1 v Alfreton TownBraintree Town 2-1 Alfreton Town | Blue Square Bet Premier |
| 15 | Sat 30 Mar 2013 | 141-2 v Kidderminster HarriersKidderminster Harriers 2-1 Braintree Town | Blue Square Bet Premier |
| 16 | Tue 9 Apr 2013 | 140-1 v Newport CountyNewport County 1-0 Braintree Town | Blue Square Bet Premier |
| 17 | Thu 11 Apr 2013 | 140-0 v DartfordDartford 0-0 Braintree Town | Blue Square Bet Premier |
| 18 | Sat 13 Apr 2013 | 142-1 v Mansfield TownBraintree Town 2-1 Mansfield Town | Blue Square Bet Premier |
| 19 | Tue 16 Apr 2013 | 141-1 v WrexhamWrexham 1-1 Braintree Town | Blue Square Bet Premier |
| 20 | Sat 20 Apr 2013 | 141-0 v BarrowBarrow 0-1 Braintree Town | Blue Square Bet Premier |
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