| 1 | Sat 3 Sep 2016 | 2-3 v Exeter CityColchester United 2-3 Exeter City | Sky Bet League Two |
| 2 | Sat 10 Sep 2016 | 313-2 v BlackpoolColchester United 3-2 Blackpool | Sky Bet League Two |
| 3 | Sat 17 Sep 2016 | 311-1 v BarnetBarnet 1-1 Colchester United | Sky Bet League Two |
| 4 | Sat 24 Sep 2016 | 311-2 v Accrington StanleyColchester United 1-2 Accrington Stanley | Sky Bet League Two |
| 5 | Tue 27 Sep 2016 | 311-1 v Crawley TownCrawley Town 1-1 Colchester United | Sky Bet League Two |
| 6 | Sat 1 Oct 2016 | 310-2 v Carlisle UnitedCarlisle United 2-0 Colchester United | Sky Bet League Two |
| 7 | Sat 8 Oct 2016 | 310-0 v Newport CountyColchester United 0-0 Newport County | Sky Bet League Two |
| 8 | Sat 22 Oct 2016 | 312-2 v MorecambeColchester United 2-2 Morecambe | Sky Bet League Two |
| 9 | Sat 29 Oct 2016 | 311-2 v Plymouth ArgylePlymouth Argyle 2-1 Colchester United | Sky Bet League Two |
| 10 | Sat 12 Nov 2016 | 310-3 v Leyton OrientColchester United 0-3 Leyton Orient | Sky Bet League Two |
| 11 | Sat 19 Nov 2016 | 311-2 v Yeovil TownYeovil Town 2-1 Colchester United | Sky Bet League Two |
| 12 | Tue 22 Nov 2016 | 313-0 v Cheltenham TownCheltenham Town 0-3 Colchester United | Sky Bet League Two |
| 13 | Sat 31 Dec 2016 | 314-2 v StevenageStevenage 2-4 Colchester United | Sky Bet League Two |
| 14 | Mon 2 Jan 2017 | 312-0 v Cheltenham TownColchester United 2-0 Cheltenham Town | Sky Bet League Two |
| 15 | Sat 7 Jan 2017 | 314-1 v Carlisle UnitedColchester United 4-1 Carlisle United | Sky Bet League Two |
| 16 | Sat 14 Jan 2017 | 311-1 v Newport CountyNewport County 1-1 Colchester United | Sky Bet League Two |
| 17 | Sat 21 Jan 2017 | 310-3 v Exeter CityExeter City 3-0 Colchester United | Sky Bet League Two |
| 18 | Sat 11 Feb 2017 | 312-1 v BarnetColchester United 2-1 Barnet | Sky Bet League Two |
| 19 | Tue 14 Feb 2017 | 312-3 v Crawley TownColchester United 2-3 Crawley Town | Sky Bet League Two |
| 20 | Tue 21 Feb 2017 | 311-0 v Wycombe WanderersColchester United 1-0 Wycombe Wanderers | Sky Bet League Two |
| 21 | Sat 25 Feb 2017 | 312-1 v Hartlepool UnitedColchester United 2-1 Hartlepool United | Sky Bet League Two |
| 22 | Tue 28 Feb 2017 | 310-1 v Grimsby TownGrimsby Town 1-0 Colchester United | Sky Bet League Two |
| 23 | Sat 4 Mar 2017 | 311-1 v Cambridge UnitedCambridge United 1-1 Colchester United | Sky Bet League Two |
| 24 | Sat 11 Mar 2017 | 310-4 v PortsmouthColchester United 0-4 Portsmouth | Sky Bet League Two |
| 25 | Sat 18 Mar 2017 | 310-2 v Crewe AlexandraCrewe Alexandra 2-0 Colchester United | Sky Bet League Two |
| 26 | Sat 25 Mar 2017 | 312-1 v Luton TownColchester United 2-1 Luton Town | Sky Bet League Two |
| 27 | Sat 1 Apr 2017 | 311-3 v Notts CountyNotts County 3-1 Colchester United | Sky Bet League Two |
| 28 | Sat 8 Apr 2017 | 314-0 v StevenageColchester United 4-0 Stevenage | Sky Bet League Two |
| 29 | Fri 14 Apr 2017 | 311-1 v Doncaster RoversColchester United 1-1 Doncaster Rovers | Sky Bet League Two |
| 30 | Mon 17 Apr 2017 | 311-1 v MorecambeMorecambe 1-1 Colchester United | Sky Bet League Two |
| 31 | Sat 22 Apr 2017 | 310-0 v Plymouth ArgyleColchester United 0-0 Plymouth Argyle | Sky Bet League Two |
| 32 | Sat 29 Apr 2017 | 313-1 v Leyton OrientLeyton Orient 1-3 Colchester United | Sky Bet League Two |
| 33 | Sat 6 May 2017 | 312-0 v Yeovil TownColchester United 2-0 Yeovil Town | Sky Bet League Two |
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