| 2016-12-31 | StevenagevColchesterLeague Two · England | 2–4 | League Two · England |
| 2016-12-26 | LutonvColchesterLeague Two · England | 0–1 | League Two · England |
| 2016-12-17 | ColchestervNotts CountyLeague Two · England | 2–1 | League Two · England |
| 2016-12-10 | MansfieldvColchesterLeague Two · England | 0–0 | League Two · England |
| 2016-11-26 | ColchestervCreweLeague Two · England | 4–0 | League Two · England |
| 2016-11-22 | CheltenhamvColchesterLeague Two · England | 0–3 | League Two · England |
| 2016-11-19 | YeovilvColchesterLeague Two · England | 2–1 | League Two · England |
| 2016-11-12 | ColchestervLeyton OrientLeague Two · England | 0–3 | League Two · England |
| 2016-10-29 | PlymouthvColchesterLeague Two · England | 2–1 | League Two · England |
| 2016-10-22 | ColchestervMorecambeLeague Two · England | 2–2 | League Two · England |
| 2016-10-15 | DoncastervColchesterLeague Two · England | 1–0 | League Two · England |
| 2016-10-08 | ColchestervNewport CountyLeague Two · England | 0–0 | League Two · England |
| 2016-10-01 | CarlislevColchesterLeague Two · England | 2–0 | League Two · England |
| 2016-09-27 | Crawley TownvColchesterLeague Two · England | 1–1 | League Two · England |
| 2016-09-24 | ColchestervAccringtonLeague Two · England | 1–2 | League Two · England |
| 2016-09-17 | BarnetvColchesterLeague Two · England | 1–1 | League Two · England |
| 2016-09-10 | ColchestervBlackpoolLeague Two · England | 3–2 | League Two · England |
| 2016-09-03 | ColchestervExeterLeague Two · England | 2–3 | League Two · England |
| 2016-08-27 | WycombevColchesterLeague Two · England | 0–2 | League Two · England |
| 2016-08-20 | PortsmouthvColchesterLeague Two · England | 2–0 | League Two · England |
| 2016-08-16 | ColchestervGrimsbyLeague Two · England | 3–2 | League Two · England |
| 2016-08-13 | ColchestervCambridgeLeague Two · England | 2–0 | League Two · England |
| 2016-08-06 | HartlepoolvColchesterLeague Two · England | 1–1 | League Two · England |
| 2016-05-08 | ColchestervRochdaleLeague One · England | 1–2 | League One · England |
| 2016-04-30 | BarnsleyvColchesterLeague One · England | 2–2 | League One · England |
| 2016-04-23 | ColchestervBurtonLeague One · England | 0–3 | League One · England |
| 2016-04-19 | CrewevColchesterLeague One · England | 1–1 | League One · England |
| 2016-04-16 | ColchestervPeterboroLeague One · England | 1–4 | League One · England |
| 2016-04-09 | BlackpoolvColchesterLeague One · England | 0–1 | League One · England |
| 2016-04-02 | ColchestervMillwallLeague One · England | 0–0 | League One · England |
| 2016-03-29 | CoventryvColchesterLeague One · England | 0–1 | League One · England |
| 2016-03-25 | ColchestervDoncasterLeague One · England | 4–1 | League One · England |
| 2016-03-19 | WalsallvColchesterLeague One · England | 2–1 | League One · England |
| 2016-03-12 | ColchestervWiganLeague One · England | 3–3 | League One · England |
| 2016-03-05 | Port ValevColchesterLeague One · England | 2–0 | League One · England |
| 2016-03-01 | BradfordvColchesterLeague One · England | 1–2 | League One · England |
| 2016-02-27 | ColchestervShrewsburyLeague One · England | 0–0 | League One · England |
| 2016-02-20 | BuryvColchesterLeague One · England | 5–2 | League One · England |
| 2016-02-16 | ColchestervChesterfieldLeague One · England | 1–1 | League One · England |
| 2016-02-13 | ColchestervSwindonLeague One · England | 1–4 | League One · England |
| 2016-02-06 | SouthendvColchesterLeague One · England | 3–0 | League One · England |
| 2016-01-23 | ScunthorpevColchesterLeague One · England | 3–0 | League One · England |
| 2016-01-19 | ColchestervFleetwood TownLeague One · England | 1–1 | League One · England |
| 2016-01-16 | ColchestervSheffield UnitedLeague One · England | 1–2 | League One · England |
| 2016-01-02 | OldhamvColchesterLeague One · England | 1–1 | League One · England |