| 1 | Tue 14 Aug 2012 | 80-3 v Yeovil TownYeovil Town 3-0 Colchester United | Capital One Cup First Round |
| 2 | Sat 18 Aug 2012 | 80-0 v Preston North EndPreston North End 0-0 Colchester United | npower League One |
| 3 | Tue 21 Aug 2012 | 82-2 v PortsmouthColchester United 2-2 Portsmouth | npower League One |
| 4 | Sat 25 Aug 2012 | 81-1 v Sheffield UnitedColchester United 1-1 Sheffield United | npower League One |
| 5 | Sat 1 Sep 2012 | 80-4 v Tranmere RoversTranmere Rovers 4-0 Colchester United | npower League One |
| 6 | Tue 18 Sep 2012 | 81-1 v Crawley TownColchester United 1-1 Crawley Town | npower League One |
| 7 | Tue 23 Oct 2012 | 82-0 v Leyton OrientLeyton Orient 0-2 Colchester United | npower League One |
| 8 | Sat 27 Oct 2012 | 82-2 v Shrewsbury TownShrewsbury Town 2-2 Colchester United | npower League One |
| 9 | Sat 15 Dec 2012 | 80-1 v BournemouthBournemouth 1-0 Colchester United | npower League One |
| 10 | Sat 22 Dec 2012 | 80-1 v WalsallWalsall 1-0 Colchester United | npower League One |
| 11 | Wed 26 Dec 2012 | 81-3 v BrentfordColchester United 1-3 Brentford | npower League One |
| 12 | Sat 6 Apr 2013 | 82-1 v Leyton OrientColchester United 2-1 Leyton Orient | npower League One |
| 13 | Sat 13 Apr 2013 | 81-3 v Notts CountyNotts County 3-1 Colchester United | npower League One |
| 14 | Tue 16 Apr 2013 | 80-2 v Milton Keynes DonsColchester United 0-2 Milton Keynes Dons | npower League One |
| 15 | Sat 20 Apr 2013 | 80-0 v Shrewsbury TownColchester United 0-0 Shrewsbury Town | npower League One |
| 16 | Sat 27 Apr 2013 | 82-0 v Carlisle UnitedCarlisle United 0-2 Colchester United | npower League One |
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