| 1 | Sat 6 Aug 2016 | 51-1 v Hartlepool UnitedHartlepool United 1-1 Colchester United | Sky Bet League Two |
| 2 | Tue 9 Aug 2016 | 50-4 v Brighton & Hove AlbionBrighton & Hove Albion 4-0 Colchester United | EFL Cup First Round |
| 3 | Sat 13 Aug 2016 | 52-0 v Cambridge UnitedColchester United 2-0 Cambridge United | Sky Bet League Two |
| 4 | Tue 16 Aug 2016 | 53-2 v Grimsby TownColchester United 3-2 Grimsby Town | Sky Bet League Two |
| 5 | Sat 20 Aug 2016 | 50-2 v PortsmouthPortsmouth 2-0 Colchester United | Sky Bet League Two |
| 6 | Sat 27 Aug 2016 | 52-0 v Wycombe WanderersWycombe Wanderers 0-2 Colchester United | Sky Bet League Two |
| 7 | Sat 3 Sep 2016 | 52-3 v Exeter CityColchester United 2-3 Exeter City | Sky Bet League Two |
| 8 | Sat 10 Sep 2016 | 53-2 v BlackpoolColchester United 3-2 Blackpool | Sky Bet League Two |
| 9 | Sat 17 Sep 2016 | 51-1 v BarnetBarnet 1-1 Colchester United | Sky Bet League Two |
| 10 | Sat 24 Sep 2016 | 51-2 v Accrington StanleyColchester United 1-2 Accrington Stanley | Sky Bet League Two |
| 11 | Tue 27 Sep 2016 | 51-1 v Crawley TownCrawley Town 1-1 Colchester United | Sky Bet League Two |
| 12 | Sat 1 Oct 2016 | 50-2 v Carlisle UnitedCarlisle United 2-0 Colchester United | Sky Bet League Two |
| 13 | Sat 15 Oct 2016 | 50-1 v Doncaster RoversDoncaster Rovers 1-0 Colchester United | Sky Bet League Two |
| 14 | Sat 22 Oct 2016 | 52-2 v MorecambeColchester United 2-2 Morecambe | Sky Bet League Two |
| 15 | Sat 29 Oct 2016 | 51-2 v Plymouth ArgylePlymouth Argyle 2-1 Colchester United | Sky Bet League Two |
| 16 | Sat 5 Nov 2016 | 51-2 v ChesterfieldColchester United 1-2 Chesterfield | Emirates FA Cup First Round |
| 17 | Sat 12 Nov 2016 | 50-3 v Leyton OrientColchester United 0-3 Leyton Orient | Sky Bet League Two |
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