| 2006-12-30 | ColchestervWolvesChampionship · England | 2–1 | Championship · England |
| 2006-12-26 | ColchestervLutonChampionship · England | 4–1 | Championship · England |
| 2006-12-23 | PrestonvColchesterChampionship · England | 1–0 | Championship · England |
| 2006-12-16 | ColchestervStokeChampionship · England | 3–0 | Championship · England |
| 2006-12-09 | Crystal PalacevColchesterChampionship · England | 1–3 | Championship · England |
| 2006-12-02 | CardiffvColchesterChampionship · England | 0–0 | Championship · England |
| 2006-11-28 | ColchestervHullChampionship · England | 5–1 | Championship · England |
| 2006-11-25 | ColchestervSouthendChampionship · England | 3–0 | Championship · England |
| 2006-11-18 | SunderlandvColchesterChampionship · England | 3–1 | Championship · England |
| 2006-11-11 | LeedsvColchesterChampionship · England | 3–0 | Championship · England |
| 2006-11-04 | ColchestervCardiffChampionship · England | 3–1 | Championship · England |
| 2006-10-31 | NorwichvColchesterChampionship · England | 1–1 | Championship · England |
| 2006-10-28 | ColchestervSouthamptonChampionship · England | 2–0 | Championship · England |
| 2006-10-23 | CoventryvColchesterChampionship · England | 2–1 | Championship · England |
| 2006-10-18 | ColchestervSheffield WedsChampionship · England | 4–0 | Championship · England |
| 2006-10-14 | WolvesvColchesterChampionship · England | 1–0 | Championship · England |
| 2006-09-29 | ColchestervIpswichChampionship · England | 1–0 | Championship · England |
| 2006-09-23 | LeicestervColchesterChampionship · England | 0–0 | Championship · England |
| 2006-09-16 | ColchestervQPRChampionship · England | 2–1 | Championship · England |
| 2006-09-12 | LutonvColchesterChampionship · England | 1–1 | Championship · England |
| 2006-09-09 | BurnleyvColchesterChampionship · England | 1–2 | Championship · England |
| 2006-08-26 | ColchestervDerbyChampionship · England | 4–3 | Championship · England |
| 2006-08-19 | West BromvColchesterChampionship · England | 2–1 | Championship · England |
| 2006-08-12 | ColchestervBarnsleyChampionship · England | 1–2 | Championship · England |
| 2006-08-08 | ColchestervPlymouthChampionship · England | 0–1 | Championship · England |
| 2006-08-05 | BirminghamvColchesterChampionship · England | 2–1 | Championship · England |
| 2006-05-06 | YeovilvColchesterLeague One · England | 0–0 | League One · England |
| 2006-04-29 | ColchestervRotherhamLeague One · England | 2–0 | League One · England |
| 2006-04-22 | BournemouthvColchesterLeague One · England | 1–2 | League One · England |
| 2006-04-17 | ColchestervTranmereLeague One · England | 1–0 | League One · England |
| 2006-04-15 | ChesterfieldvColchesterLeague One · England | 2–2 | League One · England |
| 2006-04-11 | ColchestervHartlepoolLeague One · England | 2–0 | League One · England |
| 2006-04-08 | Nott'm ForestvColchesterLeague One · England | 1–0 | League One · England |
| 2006-04-01 | ColchestervBrentfordLeague One · England | 1–1 | League One · England |
| 2006-03-25 | ScunthorpevColchesterLeague One · England | 0–0 | League One · England |
| 2006-03-21 | DoncastervColchesterLeague One · England | 0–0 | League One · England |
| 2006-03-18 | ColchestervSwindonLeague One · England | 1–0 | League One · England |
| 2006-03-11 | OldhamvColchesterLeague One · England | 1–0 | League One · England |
| 2006-03-04 | ColchestervSouthendLeague One · England | 0–3 | League One · England |
| 2006-02-25 | BarnsleyvColchesterLeague One · England | 1–0 | League One · England |
| 2006-02-14 | ColchestervWalsallLeague One · England | 0–0 | League One · England |
| 2006-02-11 | HuddersfieldvColchesterLeague One · England | 2–0 | League One · England |
| 2006-02-07 | ColchestervScunthorpeLeague One · England | 1–0 | League One · England |
| 2006-02-04 | ColchestervBradfordLeague One · England | 3–1 | League One · England |
| 2006-01-21 | ColchestervPort ValeLeague One · England | 2–1 | League One · England |
| 2006-01-17 | ColchestervBristol CityLeague One · England | 3–2 | League One · England |
| 2006-01-14 | WalsallvColchesterLeague One · England | 0–2 | League One · England |
| 2006-01-02 | ColchestervNott'm ForestLeague One · England | 3–1 | League One · England |