| 1 | Sat 6 Aug 2016 | 241-1 v Hartlepool UnitedHartlepool United 1-1 Colchester United | Sky Bet League Two |
| 2 | Tue 9 Aug 2016 | 240-4 v Brighton & Hove AlbionBrighton & Hove Albion 4-0 Colchester United | EFL Cup First Round |
| 3 | Sat 13 Aug 2016 | 242-0 v Cambridge UnitedColchester United 2-0 Cambridge United | Sky Bet League Two |
| 4 | Tue 16 Aug 2016 | 243-2 v Grimsby TownColchester United 3-2 Grimsby Town | Sky Bet League Two |
| 5 | Sat 20 Aug 2016 | 240-2 v PortsmouthPortsmouth 2-0 Colchester United | Sky Bet League Two |
| 6 | Sat 27 Aug 2016 | 242-0 v Wycombe WanderersWycombe Wanderers 0-2 Colchester United | Sky Bet League Two |
| 7 | Sat 10 Sep 2016 | 243-2 v BlackpoolColchester United 3-2 Blackpool | Sky Bet League Two |
| 8 | Sat 17 Sep 2016 | 241-1 v BarnetBarnet 1-1 Colchester United | Sky Bet League Two |
| 9 | Sat 24 Sep 2016 | 241-2 v Accrington StanleyColchester United 1-2 Accrington Stanley | Sky Bet League Two |
| 10 | Tue 27 Sep 2016 | 241-1 v Crawley TownCrawley Town 1-1 Colchester United | Sky Bet League Two |
| 11 | Sat 1 Oct 2016 | 240-2 v Carlisle UnitedCarlisle United 2-0 Colchester United | Sky Bet League Two |
| 12 | Sat 8 Oct 2016 | 240-0 v Newport CountyColchester United 0-0 Newport County | Sky Bet League Two |
| 13 | Sat 15 Oct 2016 | 240-1 v Doncaster RoversDoncaster Rovers 1-0 Colchester United | Sky Bet League Two |
| 14 | Sat 22 Oct 2016 | 242-2 v MorecambeColchester United 2-2 Morecambe | Sky Bet League Two |
| 15 | Sat 29 Oct 2016 | 241-2 v Plymouth ArgylePlymouth Argyle 2-1 Colchester United | Sky Bet League Two |
| 16 | Sat 5 Nov 2016 | 241-2 v ChesterfieldColchester United 1-2 Chesterfield | Emirates FA Cup First Round |
| 17 | Sat 12 Nov 2016 | 240-3 v Leyton OrientColchester United 0-3 Leyton Orient | Sky Bet League Two |
| 18 | Sat 19 Nov 2016 | 241-2 v Yeovil TownYeovil Town 2-1 Colchester United | Sky Bet League Two |
| 19 | Tue 22 Nov 2016 | 243-0 v Cheltenham TownCheltenham Town 0-3 Colchester United | Sky Bet League Two |
| 20 | Sat 26 Nov 2016 | 244-0 v Crewe AlexandraColchester United 4-0 Crewe Alexandra | Sky Bet League Two |
| 21 | Sat 10 Dec 2016 | 240-0 v Mansfield TownMansfield Town 0-0 Colchester United | Sky Bet League Two |
| 22 | Sat 17 Dec 2016 | 242-1 v Notts CountyColchester United 2-1 Notts County | Sky Bet League Two |
| 23 | Mon 26 Dec 2016 | 241-0 v Luton TownLuton Town 0-1 Colchester United | Sky Bet League Two |
| 24 | Mon 2 Jan 2017 | 242-0 v Cheltenham TownColchester United 2-0 Cheltenham Town | Sky Bet League Two |
| 25 | Sat 7 Jan 2017 | 244-1 v Carlisle UnitedColchester United 4-1 Carlisle United | Sky Bet League Two |
| 26 | Sat 14 Jan 2017 | 241-1 v Newport CountyNewport County 1-1 Colchester United | Sky Bet League Two |
| 27 | Sat 21 Jan 2017 | 240-3 v Exeter CityExeter City 3-0 Colchester United | Sky Bet League Two |
| 28 | Sat 4 Feb 2017 | 241-1 v BlackpoolBlackpool 1-1 Colchester United | Sky Bet League Two |
| 29 | Sat 11 Feb 2017 | 242-1 v BarnetColchester United 2-1 Barnet | Sky Bet League Two |
| 30 | Sat 18 Feb 2017 | 241-2 v Accrington StanleyAccrington Stanley 2-1 Colchester United | Sky Bet League Two |
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