| 1 | Sat 3 Aug 2013 | 41-0 v GillinghamGillingham 0-1 Colchester United | Sky Bet League One |
| 2 | Tue 6 Aug 2013 | 41-5 v Peterborough UnitedColchester United 1-5 Peterborough United | Capital One Cup First Round |
| 3 | Sat 10 Aug 2013 | 41-0 v Port ValeColchester United 1-0 Port Vale | Sky Bet League One |
| 4 | Sat 17 Aug 2013 | 41-1 v Sheffield UnitedSheffield United 1-1 Colchester United | Sky Bet League One |
| 5 | Fri 23 Aug 2013 | 41-1 v Carlisle UnitedColchester United 1-1 Carlisle United | Sky Bet League One |
| 6 | Sat 31 Aug 2013 | 41-2 v Leyton OrientColchester United 1-2 Leyton Orient | Sky Bet League One |
| 7 | Tue 3 Sep 2013 | 41-4 v Dagenham & RedbridgeDagenham & Redbridge 4-1 Colchester United | Johnstone's Paint Trophy Southern Area First Round |
| 8 | Sat 14 Sep 2013 | 42-2 v Bradford CityBradford City 2-2 Colchester United | Sky Bet League One |
| 9 | Sat 21 Sep 2013 | 41-1 v Crawley TownColchester United 1-1 Crawley Town | Sky Bet League One |
| 10 | Sat 28 Sep 2013 | 41-1 v Bristol CityBristol City 1-1 Colchester United | Sky Bet League One |
| 11 | Sat 5 Oct 2013 | 40-3 v Wolverhampton WanderersColchester United 0-3 Wolverhampton Wanderers | Sky Bet League One |
| 12 | Sat 12 Oct 2013 | 41-1 v WalsallColchester United 1-1 Walsall | Sky Bet League One |
| 13 | Sat 19 Oct 2013 | 41-3 v BrentfordBrentford 3-1 Colchester United | Sky Bet League One |
| 14 | Tue 22 Oct 2013 | 41-1 v Shrewsbury TownShrewsbury Town 1-1 Colchester United | Sky Bet League One |
| 15 | Sat 26 Oct 2013 | 41-0 v Peterborough UnitedColchester United 1-0 Peterborough United | Sky Bet League One |
| 16 | Sat 2 Nov 2013 | 42-2 v Rotherham UnitedRotherham United 2-2 Colchester United | Sky Bet League One |
| 17 | Sat 9 Nov 2013 | 42-3 v Sheffield UnitedColchester United 2-3 Sheffield United | FA Cup with Budweiser First Round |
| 18 | Sat 16 Nov 2013 | 41-2 v Swindon TownColchester United 1-2 Swindon Town | Sky Bet League One |
| 19 | Sat 23 Nov 2013 | 41-1 v Preston North EndPreston North End 1-1 Colchester United | Sky Bet League One |
| 20 | Tue 26 Nov 2013 | 43-1 v Milton Keynes DonsColchester United 3-1 Milton Keynes Dons | Sky Bet League One |
| 21 | Sat 30 Nov 2013 | 41-2 v Tranmere RoversTranmere Rovers 2-1 Colchester United | Sky Bet League One |
| 22 | Sat 14 Dec 2013 | 40-4 v Notts CountyColchester United 0-4 Notts County | Sky Bet League One |
| 23 | Sat 21 Dec 2013 | 42-0 v Oldham AthleticOldham Athletic 0-2 Colchester United | Sky Bet League One |
| 24 | Thu 26 Dec 2013 | 44-0 v StevenageColchester United 4-0 Stevenage | Sky Bet League One |
| 25 | Sun 29 Dec 2013 | 41-2 v Crewe AlexandraColchester United 1-2 Crewe Alexandra | Sky Bet League One |
| 26 | Wed 1 Jan 2014 | 40-0 v Milton Keynes DonsMilton Keynes Dons 0-0 Colchester United | Sky Bet League One |
| 27 | Sat 11 Jan 2014 | 43-0 v GillinghamColchester United 3-0 Gillingham | Sky Bet League One |
| 28 | Sat 18 Jan 2014 | 44-2 v Carlisle UnitedCarlisle United 2-4 Colchester United | Sky Bet League One |
| 29 | Tue 11 Feb 2014 | 40-2 v Port ValePort Vale 2-0 Colchester United | Sky Bet League One |
| 30 | Fri 14 Feb 2014 | 40-0 v Swindon TownSwindon Town 0-0 Colchester United | Sky Bet League One |
| 31 | Sat 22 Feb 2014 | 41-2 v Preston North EndColchester United 1-2 Preston North End | Sky Bet League One |
| 32 | Tue 25 Feb 2014 | 40-1 v Sheffield UnitedColchester United 0-1 Sheffield United | Sky Bet League One |
| 33 | Sat 1 Mar 2014 | 41-2 v Leyton OrientLeyton Orient 2-1 Colchester United | Sky Bet League One |
| 34 | Tue 4 Mar 2014 | 40-0 v Rotherham UnitedColchester United 0-0 Rotherham United | Sky Bet League One |
| 35 | Sat 8 Mar 2014 | 42-1 v Coventry CityColchester United 2-1 Coventry City | Sky Bet League One |
| 36 | Tue 11 Mar 2014 | 40-2 v Bradford CityColchester United 0-2 Bradford City | Sky Bet League One |
| 37 | Sat 15 Mar 2014 | 40-1 v Crawley TownCrawley Town 1-0 Colchester United | Sky Bet League One |
| 38 | Tue 18 Mar 2014 | 41-0 v Shrewsbury TownColchester United 1-0 Shrewsbury Town | Sky Bet League One |
| 39 | Sat 22 Mar 2014 | 42-2 v Bristol CityColchester United 2-2 Bristol City | Sky Bet League One |
| 40 | Tue 25 Mar 2014 | 42-4 v Wolverhampton WanderersWolverhampton Wanderers 4-2 Colchester United | Sky Bet League One |
| 41 | Sat 29 Mar 2014 | 40-2 v Notts CountyNotts County 2-0 Colchester United | Sky Bet League One |
| 42 | Wed 2 Apr 2014 | 40-2 v Peterborough UnitedPeterborough United 2-0 Colchester United | Sky Bet League One |
| 43 | Sat 5 Apr 2014 | 41-2 v Tranmere RoversColchester United 1-2 Tranmere Rovers | Sky Bet League One |
| 44 | Sat 12 Apr 2014 | 43-2 v StevenageStevenage 2-3 Colchester United | Sky Bet League One |
| 45 | Fri 18 Apr 2014 | 40-1 v Oldham AthleticColchester United 0-1 Oldham Athletic | Sky Bet League One |
| 46 | Mon 21 Apr 2014 | 40-0 v Crewe AlexandraCrewe Alexandra 0-0 Colchester United | Sky Bet League One |
| 47 | Sat 3 May 2014 | 41-0 v WalsallWalsall 0-1 Colchester United | Sky Bet League One |
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