| 1 | Tue 15 Aug | 16 0-2 v AFC WimbledonColchester United 0-2 AFC Wimbledon |
| 2 | Sat 19 Aug | 162-3 v Milton Keynes DonsColchester United 2-3 Milton Keynes Dons |
| 3 | Sat 26 Aug | 163-0 v GillinghamGillingham 0-3 Colchester United |
| 4 | Sat 2 Sep | 160-1 v WalsallWalsall 1-0 Colchester United |
| 5 | Sat 9 Sep | 162-0 v Tranmere RoversColchester United 2-0 Tranmere Rovers |
| 6 | Sat 16 Sep | 161-1 v Mansfield TownColchester United 1-1 Mansfield Town |
| 7 | Sat 23 Sep | 161-2 v Crewe AlexandraCrewe Alexandra 2-1 Colchester United |
| 8 | Sat 30 Sep | 165-4 v Notts CountyColchester United 5-4 Notts County |
| 9 | Tue 3 Oct | 16 1-2 v Newport CountyNewport County 2-1 Colchester United |
| 10 | Tue 24 Oct | 163-2 v Grimsby TownGrimsby Town 2-3 Colchester United |
| 11 | Sat 28 Oct | 16 1-0 v Accrington StanleyAccrington Stanley 0-1 Colchester United |
| 12 | Tue 7 Nov | 163-1 v Swindon TownColchester United 3-1 Swindon Town |
| 13 | Sat 11 Nov | 16 1-1 v Sutton UnitedColchester United 1-1 Sutton United |
| 14 | Sat 18 Nov | 160-2 v Stockport CountyStockport County 2-0 Colchester United |
| 15 | Sat 25 Nov | 161-4 v BarrowColchester United 1-4 Barrow |
| 16 | Tue 28 Nov | 161-3 v Doncaster RoversDoncaster Rovers 3-1 Colchester United |
| 17 | Sat 9 Dec | 161-2 v Crawley TownColchester United 1-2 Crawley Town |
| 18 | Sat 16 Dec | 161-2 v WrexhamWrexham 2-1 Colchester United |
| 19 | Fri 22 Dec | 16 2-1 v Salford CityColchester United 2-1 Salford City |
| 20 | Tue 26 Dec | 16 0-1 v Milton Keynes DonsMilton Keynes Dons 1-0 Colchester United |
| 21 | Fri 29 Dec | 163-5 v AFC WimbledonAFC Wimbledon 5-3 Colchester United |
| 22 | Mon 1 Jan | 160-1 v GillinghamColchester United 0-1 Gillingham |
| 23 | Sat 6 Jan | 162-2 v Swindon TownSwindon Town 2-2 Colchester United |
| 24 | Sat 13 Jan | 161-1 v Bradford CityColchester United 1-1 Bradford City |
| 25 | Sat 27 Jan | 161-0 v MorecambeMorecambe 0-1 Colchester United |
| 26 | Sat 3 Feb | 163-3 v Forest Green RoversColchester United 3-3 Forest Green Rovers |
| 27 | Sat 24 Feb | 16 1-1 v Sutton UnitedSutton United 1-1 Colchester United |
| 28 | Tue 27 Feb | 161-1 v Salford CitySalford City 1-1 Colchester United |
| 29 | Sat 9 Mar | 160-2 v BarrowBarrow 2-0 Colchester United |
| 30 | Sat 16 Mar | 161-1 v WalsallColchester United 1-1 Walsall |
| 31 | Sat 23 Mar | 161-1 v Mansfield TownMansfield Town 1-1 Colchester United |
| 32 | Fri 29 Mar | 162-1 v Newport CountyColchester United 2-1 Newport County |
| 33 | Mon 1 Apr | 161-1 v Tranmere RoversTranmere Rovers 1-1 Colchester United |
| 34 | Sat 6 Apr | 161-2 v WrexhamColchester United 1-2 Wrexham |
| 35 | Tue 9 Apr | 161-2 v Stockport CountyColchester United 1-2 Stockport County |
| 36 | Sat 13 Apr | 163-2 v Crawley TownCrawley Town 2-3 Colchester United |
| 37 | Tue 16 Apr | 162-0 v Grimsby TownColchester United 2-0 Grimsby Town |
| 38 | Sat 20 Apr | 16 0-1 v Notts CountyNotts County 1-0 Colchester United |
| 39 | Tue 23 Apr | 161-4 v Doncaster RoversColchester United 1-4 Doncaster Rovers |
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