| 1 | Sat 6 Aug 2016 | 1-1 v Hartlepool UnitedHartlepool United 1-1 Colchester United | Sky Bet League Two |
| 2 | Sat 13 Aug 2016 | 332-0 v Cambridge UnitedColchester United 2-0 Cambridge United | Sky Bet League Two |
| 3 | Tue 16 Aug 2016 | 333-2 v Grimsby TownColchester United 3-2 Grimsby Town | Sky Bet League Two |
| 4 | Sat 20 Aug 2016 | 330-2 v PortsmouthPortsmouth 2-0 Colchester United | Sky Bet League Two |
| 5 | Sat 27 Aug 2016 | 332-0 v Wycombe WanderersWycombe Wanderers 0-2 Colchester United | Sky Bet League Two |
| 6 | Tue 30 Aug 2016 | 330-1 v Crawley TownCrawley Town 1-0 Colchester United | Checkatrade Trophy Southern Group E |
| 7 | Sat 3 Sep 2016 | 332-3 v Exeter CityColchester United 2-3 Exeter City | Sky Bet League Two |
| 8 | Sat 10 Sep 2016 | 333-2 v BlackpoolColchester United 3-2 Blackpool | Sky Bet League Two |
| 9 | Sat 17 Sep 2016 | 331-1 v BarnetBarnet 1-1 Colchester United | Sky Bet League Two |
| 10 | Sat 24 Sep 2016 | 331-2 v Accrington StanleyColchester United 1-2 Accrington Stanley | Sky Bet League Two |
| 11 | Tue 27 Sep 2016 | 331-1 v Crawley TownCrawley Town 1-1 Colchester United | Sky Bet League Two |
| 12 | Sat 1 Oct 2016 | 330-2 v Carlisle UnitedCarlisle United 2-0 Colchester United | Sky Bet League Two |
| 13 | Sat 8 Oct 2016 | 330-0 v Newport CountyColchester United 0-0 Newport County | Sky Bet League Two |
| 14 | Sat 8 Apr 2017 | 334-0 v StevenageColchester United 4-0 Stevenage | Sky Bet League Two |
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