| 1 | Tue 14 Aug 2012 | 10-3 v Yeovil TownYeovil Town 3-0 Colchester United | Capital One Cup First Round |
| 2 | Sat 18 Aug 2012 | 10-0 v Preston North EndPreston North End 0-0 Colchester United | npower League One |
| 3 | Tue 21 Aug 2012 | 12-2 v PortsmouthColchester United 2-2 Portsmouth | npower League One |
| 4 | Sat 25 Aug 2012 | 11-1 v Sheffield UnitedColchester United 1-1 Sheffield United | npower League One |
| 5 | Sat 1 Sep 2012 | 10-4 v Tranmere RoversTranmere Rovers 4-0 Colchester United | npower League One |
| 6 | Sat 8 Sep 2012 | 10-1 v BrentfordBrentford 1-0 Colchester United | npower League One |
| 7 | Sat 15 Sep 2012 | 11-2 v Doncaster RoversColchester United 1-2 Doncaster Rovers | npower League One |
| 8 | Tue 18 Sep 2012 | 11-1 v Crawley TownColchester United 1-1 Crawley Town | npower League One |
| 9 | Sat 22 Sep 2012 | 10-1 v Scunthorpe UnitedScunthorpe United 1-0 Colchester United | npower League One |
| 10 | Sat 29 Sep 2012 | 13-1 v Hartlepool UnitedColchester United 3-1 Hartlepool United | npower League One |
| 11 | Tue 2 Oct 2012 | 11-0 v Swindon TownSwindon Town 0-1 Colchester United | npower League One |
| 12 | Sat 6 Oct 2012 | 11-3 v Yeovil TownYeovil Town 3-1 Colchester United | npower League One |
| 13 | Sat 13 Oct 2012 | 11-0 v StevenageColchester United 1-0 Stevenage | npower League One |
| 14 | Sat 20 Oct 2012 | 12-0 v Carlisle UnitedColchester United 2-0 Carlisle United | npower League One |
| 15 | Tue 23 Oct 2012 | 12-0 v Leyton OrientLeyton Orient 0-2 Colchester United | npower League One |
| 16 | Sat 27 Oct 2012 | 12-2 v Shrewsbury TownShrewsbury Town 2-2 Colchester United | npower League One |
| 17 | Sat 3 Nov 2012 | 11-3 v Chelmsford CityChelmsford City 3-1 Colchester United | FA Cup with Budweiser First Round |
| 18 | Tue 6 Nov 2012 | 10-2 v Notts CountyColchester United 0-2 Notts County | npower League One |
| 19 | Sat 8 Dec 2012 | 10-2 v Oldham AthleticColchester United 0-2 Oldham Athletic | npower League One |
| 20 | Sat 15 Dec 2012 | 10-1 v BournemouthBournemouth 1-0 Colchester United | npower League One |
| 21 | Sat 22 Dec 2012 | 10-1 v WalsallWalsall 1-0 Colchester United | npower League One |
| 22 | Wed 26 Dec 2012 | 11-3 v BrentfordColchester United 1-3 Brentford | npower League One |
| 23 | Tue 1 Jan 2013 | 10-3 v Crawley TownCrawley Town 3-0 Colchester United | npower League One |
| 24 | Sat 5 Jan 2013 | 10-1 v Doncaster RoversDoncaster Rovers 1-0 Colchester United | npower League One |
| 25 | Sat 12 Jan 2013 | 11-2 v Scunthorpe UnitedColchester United 1-2 Scunthorpe United | npower League One |
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