| 1 | Sat 11 Aug 2012 | 222-2 v HydeBraintree Town 2-2 Hyde | Blue Square Bet Premier |
| 2 | Tue 14 Aug 2012 | 221-0 v Ebbsfleet UnitedEbbsfleet United 0-1 Braintree Town | Blue Square Bet Premier |
| 3 | Sat 18 Aug 2012 | 220-3 v AFC Telford UnitedAFC Telford United 3-0 Braintree Town | Blue Square Bet Premier |
| 4 | Sat 25 Aug 2012 | 221-2 v Newport CountyBraintree Town 1-2 Newport County | Blue Square Bet Premier |
| 5 | Tue 28 Aug 2012 | 224-1 v WokingWoking 1-4 Braintree Town | Blue Square Bet Premier |
| 6 | Sat 1 Sep 2012 | 222-1 v TamworthBraintree Town 2-1 Tamworth | Blue Square Bet Premier |
| 7 | Tue 4 Sep 2012 | 221-1 v Kidderminster HarriersBraintree Town 1-1 Kidderminster Harriers | Blue Square Bet Premier |
| 8 | Sat 8 Sep 2012 | 221-2 v Macclesfield TownMacclesfield Town 2-1 Braintree Town | Blue Square Bet Premier |
| 9 | Sat 15 Sep 2012 | 220-2 v Mansfield TownMansfield Town 2-0 Braintree Town | Blue Square Bet Premier |
| 10 | Sat 22 Sep 2012 | 220-0 v Stockport CountyBraintree Town 0-0 Stockport County | Blue Square Bet Premier |
| 11 | Tue 25 Sep 2012 | 220-2 v DartfordBraintree Town 0-2 Dartford | Blue Square Bet Premier |
| 12 | Sat 29 Sep 2012 | 221-1 v Alfreton TownAlfreton Town 1-1 Braintree Town | Blue Square Bet Premier |
| 13 | Sat 6 Oct 2012 | 222-3 v BarrowBraintree Town 2-3 Barrow | Blue Square Bet Premier |
| 14 | Tue 9 Oct 2012 | 223-2 v Luton TownLuton Town 2-3 Braintree Town | Blue Square Bet Premier |
| 15 | Tue 6 Nov 2012 | 220-3 v Lincoln CityLincoln City 3-0 Braintree Town | Blue Square Bet Premier |
| 16 | Sat 10 Nov 2012 | 222-1 v GatesheadBraintree Town 2-1 Gateshead | Blue Square Bet Premier |
| 17 | Tue 13 Nov 2012 | 220-3 v Tranmere RoversBraintree Town 0-3 Tranmere Rovers | FA Cup with Budweiser First Round |
| 18 | Sat 17 Nov 2012 | 220-3 v Grimsby TownGrimsby Town 3-0 Braintree Town | Blue Square Bet Premier |
| 19 | Tue 20 Nov 2012 | 221-5 v WrexhamBraintree Town 1-5 Wrexham | Blue Square Bet Premier |
| 20 | Sat 8 Dec 2012 | 222-0 v SouthportSouthport 0-2 Braintree Town | Blue Square Bet Premier |
| 21 | Tue 18 Dec 2012 | 223-1 v Forest Green RoversBraintree Town 3-1 Forest Green Rovers | Blue Square Bet Premier |
| 22 | Wed 26 Dec 2012 | 220-3 v Cambridge UnitedBraintree Town 0-3 Cambridge United | Blue Square Bet Premier |
| 23 | Tue 1 Jan 2013 | 220-1 v Cambridge UnitedCambridge United 1-0 Braintree Town | Blue Square Bet Premier |
| 24 | Wed 3 Apr 2013 | 221-3 v SouthportBraintree Town 1-3 Southport | Blue Square Bet Premier |
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