| 1 | Sat 6 Aug 2016 | 41-1 v Hartlepool UnitedHartlepool United 1-1 Colchester United | Sky Bet League Two |
| 2 | Tue 9 Aug 2016 | 40-4 v Brighton & Hove AlbionBrighton & Hove Albion 4-0 Colchester United | EFL Cup First Round |
| 3 | Sat 13 Aug 2016 | 42-0 v Cambridge UnitedColchester United 2-0 Cambridge United | Sky Bet League Two |
| 4 | Tue 16 Aug 2016 | 43-2 v Grimsby TownColchester United 3-2 Grimsby Town | Sky Bet League Two |
| 5 | Sat 20 Aug 2016 | 40-2 v PortsmouthPortsmouth 2-0 Colchester United | Sky Bet League Two |
| 6 | Sat 27 Aug 2016 | 42-0 v Wycombe WanderersWycombe Wanderers 0-2 Colchester United | Sky Bet League Two |
| 7 | Tue 30 Aug 2016 | 40-1 v Crawley TownCrawley Town 1-0 Colchester United | Checkatrade Trophy Southern Group E |
| 8 | Sat 3 Sep 2016 | 42-3 v Exeter CityColchester United 2-3 Exeter City | Sky Bet League Two |
| 9 | Sat 10 Sep 2016 | 43-2 v BlackpoolColchester United 3-2 Blackpool | Sky Bet League Two |
| 10 | Sat 12 Nov 2016 | 40-3 v Leyton OrientColchester United 0-3 Leyton Orient | Sky Bet League Two |
| 11 | Sat 19 Nov 2016 | 41-2 v Yeovil TownYeovil Town 2-1 Colchester United | Sky Bet League Two |
| 12 | Tue 22 Nov 2016 | 43-0 v Cheltenham TownCheltenham Town 0-3 Colchester United | Sky Bet League Two |
| 13 | Sat 26 Nov 2016 | 44-0 v Crewe AlexandraColchester United 4-0 Crewe Alexandra | Sky Bet League Two |
| 14 | Sat 10 Dec 2016 | 40-0 v Mansfield TownMansfield Town 0-0 Colchester United | Sky Bet League Two |
| 15 | Sat 17 Dec 2016 | 42-1 v Notts CountyColchester United 2-1 Notts County | Sky Bet League Two |
| 16 | Mon 26 Dec 2016 | 41-0 v Luton TownLuton Town 0-1 Colchester United | Sky Bet League Two |
| 17 | Sat 31 Dec 2016 | 44-2 v StevenageStevenage 2-4 Colchester United | Sky Bet League Two |
| 18 | Mon 2 Jan 2017 | 42-0 v Cheltenham TownColchester United 2-0 Cheltenham Town | Sky Bet League Two |
| 19 | Sat 7 Jan 2017 | 44-1 v Carlisle UnitedColchester United 4-1 Carlisle United | Sky Bet League Two |
| 20 | Sat 14 Jan 2017 | 41-1 v Newport CountyNewport County 1-1 Colchester United | Sky Bet League Two |
| 21 | Sat 21 Jan 2017 | 40-3 v Exeter CityExeter City 3-0 Colchester United | Sky Bet League Two |
| 22 | Sat 4 Feb 2017 | 41-1 v BlackpoolBlackpool 1-1 Colchester United | Sky Bet League Two |
| 23 | Sat 11 Feb 2017 | 42-1 v BarnetColchester United 2-1 Barnet | Sky Bet League Two |
| 24 | Tue 14 Feb 2017 | 42-3 v Crawley TownColchester United 2-3 Crawley Town | Sky Bet League Two |
| 25 | Sat 18 Feb 2017 | 41-2 v Accrington StanleyAccrington Stanley 2-1 Colchester United | Sky Bet League Two |
| 26 | Tue 21 Feb 2017 | 41-0 v Wycombe WanderersColchester United 1-0 Wycombe Wanderers | Sky Bet League Two |
| 27 | Sat 25 Feb 2017 | 42-1 v Hartlepool UnitedColchester United 2-1 Hartlepool United | Sky Bet League Two |
| 28 | Tue 28 Feb 2017 | 40-1 v Grimsby TownGrimsby Town 1-0 Colchester United | Sky Bet League Two |
| 29 | Sat 4 Mar 2017 | 41-1 v Cambridge UnitedCambridge United 1-1 Colchester United | Sky Bet League Two |
| 30 | Sat 11 Mar 2017 | 40-4 v PortsmouthColchester United 0-4 Portsmouth | Sky Bet League Two |
| 31 | Tue 14 Mar 2017 | 42-0 v Mansfield TownColchester United 2-0 Mansfield Town | Sky Bet League Two |
| 32 | Sat 18 Mar 2017 | 40-2 v Crewe AlexandraCrewe Alexandra 2-0 Colchester United | Sky Bet League Two |
| 33 | Sat 25 Mar 2017 | 42-1 v Luton TownColchester United 2-1 Luton Town | Sky Bet League Two |
| 34 | Sat 1 Apr 2017 | 41-3 v Notts CountyNotts County 3-1 Colchester United | Sky Bet League Two |
| 35 | Sat 8 Apr 2017 | 44-0 v StevenageColchester United 4-0 Stevenage | Sky Bet League Two |
| 36 | Fri 14 Apr 2017 | 41-1 v Doncaster RoversColchester United 1-1 Doncaster Rovers | Sky Bet League Two |
| 37 | Sat 22 Apr 2017 | 40-0 v Plymouth ArgyleColchester United 0-0 Plymouth Argyle | Sky Bet League Two |
| 38 | Sat 29 Apr 2017 | 43-1 v Leyton OrientLeyton Orient 1-3 Colchester United | Sky Bet League Two |
| 39 | Sat 6 May 2017 | 42-0 v Yeovil TownColchester United 2-0 Yeovil Town | Sky Bet League Two |
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