| 1 | Sat 11 Aug 2012 | 62-2 v HydeBraintree Town 2-2 Hyde | Blue Square Bet Premier |
| 2 | Tue 14 Aug 2012 | 61-0 v Ebbsfleet UnitedEbbsfleet United 0-1 Braintree Town | Blue Square Bet Premier |
| 3 | Sat 18 Aug 2012 | 60-3 v AFC Telford UnitedAFC Telford United 3-0 Braintree Town | Blue Square Bet Premier |
| 4 | Sat 25 Aug 2012 | 61-2 v Newport CountyBraintree Town 1-2 Newport County | Blue Square Bet Premier |
| 5 | Tue 28 Aug 2012 | 64-1 v WokingWoking 1-4 Braintree Town | Blue Square Bet Premier |
| 6 | Sat 1 Sep 2012 | 62-1 v TamworthBraintree Town 2-1 Tamworth | Blue Square Bet Premier |
| 7 | Tue 4 Sep 2012 | 61-1 v Kidderminster HarriersBraintree Town 1-1 Kidderminster Harriers | Blue Square Bet Premier |
| 8 | Sat 8 Sep 2012 | 61-2 v Macclesfield TownMacclesfield Town 2-1 Braintree Town | Blue Square Bet Premier |
| 9 | Sat 15 Sep 2012 | 60-2 v Mansfield TownMansfield Town 2-0 Braintree Town | Blue Square Bet Premier |
| 10 | Sat 22 Sep 2012 | 60-0 v Stockport CountyBraintree Town 0-0 Stockport County | Blue Square Bet Premier |
| 11 | Tue 25 Sep 2012 | 60-2 v DartfordBraintree Town 0-2 Dartford | Blue Square Bet Premier |
| 12 | Sat 6 Oct 2012 | 62-3 v BarrowBraintree Town 2-3 Barrow | Blue Square Bet Premier |
| 13 | Tue 9 Oct 2012 | 63-2 v Luton TownLuton Town 2-3 Braintree Town | Blue Square Bet Premier |
| 14 | Tue 6 Nov 2012 | 60-3 v Lincoln CityLincoln City 3-0 Braintree Town | Blue Square Bet Premier |
| 15 | Sat 10 Nov 2012 | 62-1 v GatesheadBraintree Town 2-1 Gateshead | Blue Square Bet Premier |
| 16 | Tue 13 Nov 2012 | 60-3 v Tranmere RoversBraintree Town 0-3 Tranmere Rovers | FA Cup with Budweiser First Round |
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