| 1999-12-26 | GillinghamvColchesterLeague One · England | 2–1 | League One · England |
| 1999-12-17 | ColchestervLutonLeague One · England | 3–0 | League One · England |
| 1999-12-11 | Bristol RvsvColchesterLeague One · England | 2–1 | League One · England |
| 1999-12-03 | ColchestervChesterfieldLeague One · England | 1–0 | League One · England |
| 1999-11-27 | StokevColchesterLeague One · England | 1–1 | League One · England |
| 1999-11-23 | ColchestervCardiffLeague One · England | 0–3 | League One · England |
| 1999-11-19 | ColchestervBrentfordLeague One · England | 0–3 | League One · England |
| 1999-11-14 | OldhamvColchesterLeague One · England | 1–2 | League One · England |
| 1999-11-06 | ColchestervPrestonLeague One · England | 2–2 | League One · England |
| 1999-11-02 | OxfordvColchesterLeague One · England | 1–1 | League One · England |
| 1999-10-26 | ColchestervWiganLeague One · England | 2–2 | League One · England |
| 1999-10-23 | ColchestervMillwallLeague One · England | 1–2 | League One · England |
| 1999-10-19 | Bristol CityvColchesterLeague One · England | 1–1 | League One · England |
| 1999-10-15 | CambridgevColchesterLeague One · England | 5–2 | League One · England |
| 1999-10-01 | ColchestervWrexhamLeague One · England | 2–2 | League One · England |
| 1999-09-25 | MillwallvColchesterLeague One · England | 1–0 | League One · England |
| 1999-09-18 | BurnleyvColchesterLeague One · England | 3–0 | League One · England |
| 1999-09-11 | ColchestervScunthorpeLeague One · England | 0–1 | League One · England |
| 1999-08-30 | BuryvColchesterLeague One · England | 5–2 | League One · England |
| 1999-08-28 | ColchestervReadingLeague One · England | 3–2 | League One · England |
| 1999-08-21 | BournemouthvColchesterLeague One · England | 4–0 | League One · England |
| 1999-08-14 | ColchestervNotts CountyLeague One · England | 0–3 | League One · England |
| 1999-08-07 | ChesterfieldvColchesterLeague One · England | 0–1 | League One · England |
| 1999-05-08 | BlackpoolvColchesterLeague One · England | 2–1 | League One · England |
| 1999-05-01 | ColchestervLincolnLeague One · England | 1–3 | League One · England |
| 1999-04-27 | ColchestervBournemouthLeague One · England | 2–1 | League One · England |
| 1999-04-24 | NorthamptonvColchesterLeague One · England | 3–3 | League One · England |
| 1999-04-16 | ColchestervNotts CountyLeague One · England | 2–1 | League One · England |
| 1999-04-14 | MillwallvColchesterLeague One · England | 2–0 | League One · England |
| 1999-04-10 | ColchestervWalsallLeague One · England | 1–0 | League One · England |
| 1999-04-05 | BurnleyvColchesterLeague One · England | 3–1 | League One · England |
| 1999-04-02 | ColchestervPrestonLeague One · England | 1–0 | League One · England |
| 1999-03-27 | BournemouthvColchesterLeague One · England | 2–1 | League One · England |
| 1999-03-20 | ColchestervMan CityLeague One · England | 0–1 | League One · England |
| 1999-03-13 | MacclesfieldvColchesterLeague One · England | 2–0 | League One · England |
| 1999-03-09 | ColchestervOldhamLeague One · England | 2–2 | League One · England |
| 1999-03-06 | WycombevColchesterLeague One · England | 2–2 | League One · England |
| 1999-02-27 | ColchestervReadingLeague One · England | 1–1 | League One · England |
| 1999-02-20 | GillinghamvColchesterLeague One · England | 1–1 | League One · England |
| 1999-02-12 | ColchestervWiganLeague One · England | 2–1 | League One · England |
| 1999-02-05 | ColchestervYorkLeague One · England | 2–1 | League One · England |
| 1999-01-30 | Bristol RvsvColchesterLeague One · England | 1–1 | League One · England |
| 1999-01-23 | StokevColchesterLeague One · England | 3–3 | League One · England |
| 1999-01-15 | ColchestervWrexhamLeague One · England | 1–3 | League One · England |
| 1999-01-09 | ChesterfieldvColchesterLeague One · England | 3–1 | League One · England |
| 1999-01-02 | ColchestervLutonLeague One · England | 2–2 | League One · England |