| 1 | Sat 8 Sep 2012 | 161-2 v Macclesfield TownMacclesfield Town 2-1 Braintree Town | Blue Square Bet Premier |
| 2 | Sat 15 Sep 2012 | 160-2 v Mansfield TownMansfield Town 2-0 Braintree Town | Blue Square Bet Premier |
| 3 | Sat 22 Sep 2012 | 160-0 v Stockport CountyBraintree Town 0-0 Stockport County | Blue Square Bet Premier |
| 4 | Tue 25 Sep 2012 | 160-2 v DartfordBraintree Town 0-2 Dartford | Blue Square Bet Premier |
| 5 | Sat 29 Sep 2012 | 161-1 v Alfreton TownAlfreton Town 1-1 Braintree Town | Blue Square Bet Premier |
| 6 | Sat 6 Oct 2012 | 162-3 v BarrowBraintree Town 2-3 Barrow | Blue Square Bet Premier |
| 7 | Tue 9 Oct 2012 | 163-2 v Luton TownLuton Town 2-3 Braintree Town | Blue Square Bet Premier |
| 8 | Tue 6 Nov 2012 | 160-3 v Lincoln CityLincoln City 3-0 Braintree Town | Blue Square Bet Premier |
| 9 | Sat 10 Nov 2012 | 162-1 v GatesheadBraintree Town 2-1 Gateshead | Blue Square Bet Premier |
| 10 | Tue 13 Nov 2012 | 160-3 v Tranmere RoversBraintree Town 0-3 Tranmere Rovers | FA Cup with Budweiser First Round |
| 11 | Sat 17 Nov 2012 | 160-3 v Grimsby TownGrimsby Town 3-0 Braintree Town | Blue Square Bet Premier |
| 12 | Tue 20 Nov 2012 | 161-5 v WrexhamBraintree Town 1-5 Wrexham | Blue Square Bet Premier |
| 13 | Tue 18 Dec 2012 | 163-1 v Forest Green RoversBraintree Town 3-1 Forest Green Rovers | Blue Square Bet Premier |
| 14 | Wed 26 Dec 2012 | 160-3 v Cambridge UnitedBraintree Town 0-3 Cambridge United | Blue Square Bet Premier |
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