| Season |
Competition |
Round Reached |
Date |
Home |
Score |
Away |
| 2012/2013 | F.A. Cup | 1st Round | Sat 03 Nov | Chelmsford C. | 3 - 1 | Colchester U. |
| League Cup | 1st Round | Tue 14 Aug | Yeovil Town | 3 - 0 | Colchester U. |
| (Associate Members) | Southern 2nd Round | Tue 09 Oct | Northampton | 2 - 1 | Colchester U. |
| 2011/2012 | F.A. Cup | 2nd Round | Sat 03 Dec | Colchester U. | 0 - 1 | Swindon Town |
| League Cup | 1st Round | Tue 09 Aug | Wycombe Wdrs. | 3 - 3 | Colchester U. |
| after extra time, 90 minutes 2-2, Wycombe Wanderers won 5-4 on penalties |
| (Associate Members) | Southern 1st Round | Tue 30 Aug | Colchester U. | 1 - 3 | Barnet |
| 2010/2011 | F.A. Cup | 3rd Round | Sat 08 Jan | Swansea City | 4 - 0 | Colchester U. |
| League Cup | 2nd Round | Tue 24 Aug | Sunderland | 2 - 0 | Colchester U. |
| (Associate Members) | Southern 2nd Round | Tue 05 Oct | Colchester U. | 0 - 2 | Wycombe Wdrs. |
| 2009/2010 | F.A. Cup | 3rd Round | Sat 02 Jan | Preston N.E. | 7 - 0 | Colchester U. |
| League Cup | 1st Round | Tue 11 Aug | Colchester U. | 1 - 2 | Leyton Orient |
| (Associate Members) | Southern 1st Round | Tue 01 Sep | Gillingham | 1 - 1 | Colchester U. |
| after extra time, 90 minutes 1-1, Gillingham won 4-3 on penalties |
| 2008/2009 | F.A. Cup | 1st Round | Sat 08 Nov | Colchester U. | 0 - 1 | Leyton Orient |
| League Cup | 2nd Round | Tue 26 Aug | Ipswich Town | 2 - 1 | Colchester U. |
| (Associate Members) | Southern Semi-Final | Tue 16 Dec | Luton Town | 1 - 0 | Colchester U. |
| 2007/2008 | F.A. Cup | 3rd Round | Sat 05 Jan | Colchester U. | 1 - 3 | Peterborough |
| League Cup | 1st Round | Tue 14 Aug | Shrewsbury Tn. | 1 - 0 | Colchester U. |
| after extra time, 90 minutes 0-0 |
| 2006/2007 | F.A. Cup | 3rd Round | Tue 09 Jan | Barnet | 2 - 1 | Colchester U. |
| League Cup | 1st Round | Tue 22 Aug | Milton Keynes | 1 - 0 | Colchester U. |
| after extra time, 90 minutes 0-0 |
| 2005/2006 | F.A. Cup | 5th Round | Sun 19 Feb | Chelsea | 3 - 1 | Colchester U. |
| League Cup | 1st Round | Wed 24 Aug | Colchester U. | 0 - 2 | Cardiff City |
| (Associate Members) | Southern Final | Tue 14 Mar | Colchester U. | 1 - 2 | Swansea City |
| Swansea City won 3-1 on aggregate |
| 2004/2005 | F.A. Cup | 4th Round | Sat 29 Jan | Blackburn R. | 3 - 0 | Colchester U. |
| League Cup | 3rd Round | Wed 27 Oct | Southampton | 3 - 2 | Colchester U. |
| (Associate Members) | Southern 1st Round | Wed 29 Sep | Colchester U. | 1 - 1 | Southend Utd. |
| after extra time, 90 minutes 1-1, Southend United won 5-3 on penalties |
| 2003/2004 | F.A. Cup | 5th Round | Sun 15 Feb | Sheff. Utd. | 1 - 0 | Colchester U. |
| League Cup | 2nd Round | Tue 23 Sep | Rotherham U. | 1 - 0 | Colchester U. |
| (Associate Members) | Southern Final | Tue 17 Feb | Southend Utd. | 1 - 1 | Colchester U. |
| Southend United won 4-3 on aggregate |
| 2002/2003 | F.A. Cup | 1st Round | Sat 16 Nov | Colchester U. | 0 - 1 | Chester City |
| League Cup | 1st Round | Wed 11 Sep | Coventry City | 3 - 0 | Colchester U. |
| (Associate Members) | Southern 1st Round | Tue 22 Oct | Cheltenham T. | 4 - 1 | Colchester U. |
| 2001/2002 | F.A. Cup | 1st Round Replay | Tue 27 Nov | York City | 2 - 2 | Colchester U. |
| after extra time, 90 minutes 2-2, York City won 3-2 on penalties |
| League Cup | 2nd Round | Tue 11 Sep | Colchester U. | 1 - 3 | Barnsley |
| (Associate Members) | Southern 2nd Round | Tue 30 Oct | Reading | 2 - 1 | Colchester U. |
| 2000/2001 | F.A. Cup | 1st Round | Sat 18 Nov | Yeovil Town | 5 - 1 | Colchester U. |
| League Cup | 2nd Round | Wed 27 Sep | Colchester U. | 0 - 1 | Sheff. Utd. |
| (Associate Members) | Southern 1st Round | Tue 05 Dec | Cambridge U. | 2 - 0 | Colchester U. |
| 1999/2000 | F.A. Cup | 1st Round | Sat 30 Oct | Swansea City | 2 - 1 | Colchester U. |
| League Cup | 1st Round | Tue 24 Aug | Crystal Palace | 3 - 1 | Colchester U. |
| Crystal Palace won 5-3 on aggregate |
| (Associate Members) | Southern 1st Round | Tue 07 Dec | Swansea City | 3 - 1 | Colchester U. |
| 1998/1999 | F.A. Cup | 1st Round | Sat 14 Nov | Bedlington | 4 - 1 | Colchester U. |
| League Cup | 1st Round | Tue 18 Aug | Colchester U. | 3 - 2 | Bournemouth |
| Bournemouth won 4-3 on aggregate |
| (Associate Members) | Southern 1st Round | Sat 05 Dec | Colchester U. | 1 - 5 | Gillingham |
| 1997/1998 | F.A. Cup | 2nd Round Replay | Tue 16 Dec | Hereford Utd. | 1 - 1 | Colchester U. |
| after extra time, 90 minutes 1-1, Hereford United won 5-4 on penalties |
| League Cup | 1st Round | Tue 26 Aug | Luton Town | 1 - 1 | Colchester U. |
| Luton Town won 2-1 on aggregate |
| (Associate Members) | Southern 1st Round | Tue 09 Dec | Leyton Orient | 1 - 0 | Colchester U. |
| 1996/1997 | F.A. Cup | 1st Round | Sat 16 Nov | Colchester U. | 1 - 2 | Wycombe Wdrs. |
| League Cup | 2nd Round | Tue 24 Sep | Colchester U. | 0 - 2 | Huddersfield |
| Huddersfield Town won 3-1 on aggregate |
| (Associate Members) | Final | Sun 20 Apr | Carlisle Utd. | 0 - 0 | Colchester U. |
| at Wembley, after extra time, Carlisle United won 4-3 on penalties |
| 1995/1996 | F.A. Cup | 1st Round | Sat 11 Nov | Gravesend | 2 - 0 | Colchester U. |
| League Cup | 1st Round | Tue 22 Aug | Bristol City | 2 - 1 | Colchester U. |
| after extra time, 90 minutes 2-1, aggregate 3-3, Bristol City won 5-3 on penalties |
| (Associate Members) | Southern Quarter-Final | Tue 09 Jan | Peterborough | 3 - 2 | Colchester U. |
| 1994/1995 | F.A. Cup | 3rd Round | Sat 07 Jan | Wimbledon | 1 - 0 | Colchester U. |
| League Cup | 1st Round | Tue 23 Aug | Brentford | 2 - 0 | Colchester U. |
| Brentford won 4-0 on aggregate |
| (Associate Members) | Southern Preliminary Round Group Five | Tue 08 Nov | Fulham | 3 - 2 | Colchester U. |
| 1993/1994 | F.A. Cup | 1st Round | Sat 13 Nov | Colchester U. | 3 - 4 | Sutton Utd. |
| League Cup | 1st Round | Tue 24 Aug | Colchester U. | 1 - 2 | Fulham |
| Fulham won 4-2 on aggregate |
| (Associate Members) | Southern Quarter-Final | Tue 11 Jan | Colchester U. | 0 - 1 | Wycombe Wdrs. |
| 1992/1993 | F.A. Cup | 2nd Round Replay | Wed 16 Dec | Colchester U. | 2 - 3 | Gillingham |
| League Cup | 1st Round | Wed 26 Aug | Brighton & HA | 1 - 0 | Colchester U. |
| Brighton & Hove Albion won 2-1 on aggregate |
| (Associate Members) | Southern Preliminary Round Group One | Mon 21 Dec | Barnet | 4 - 2 | Colchester U. |
| 1991/1992 | F.A. Cup | 1st Round Replay | Wed 27 Nov | Exeter City | 0 - 0 | Colchester U. |
| after extra time, 90 minutes 0-0, Exeter City won 4-2 on penalties |
| 1990/1991 | F.A. Cup | 2nd Round Replay | Mon 17 Dec | Leyton Orient | 4 - 1 | Colchester U. |
| 1989/1990 | F.A. Cup | 2nd Round | Sat 09 Dec | Colchester U. | 0 - 2 | Birmingham C. |
| League Cup | 1st Round | Tue 29 Aug | Southend Utd. | 2 - 1 | Colchester U. |
| Southend United won 6-4 on aggregate |
| (Associate Members) | Southern Preliminary Round Group Six | Wed 10 Jan | Maidstone Utd. | 2 - 1 | Colchester U. |
| 1988/1989 | F.A. Cup | 4th Round Replay | Tue 31 Jan | Colchester U. | 0 - 2 | Sheff. Utd. |
| League Cup | 1st Round | Tue 06 Sep | Northampton | 5 - 0 | Colchester U. |
| Northampton Town won 5-0 on aggregate |
| (Associate Members) | Southern Quarter-Final | Tue 14 Feb | Colchester U. | 0 - 1 | Hereford Utd. |
| 1987/1988 | F.A. Cup | 3rd Round | Mon 11 Jan | Plymouth Arg. | 2 - 0 | Colchester U. |
| League Cup | 1st Round | Tue 25 Aug | Colchester U. | 0 - 2 | Fulham |
| Fulham won 5-1 on aggregate |
| (Associate Members) | Southern Quarter-Final | Tue 09 Feb | Colchester U. | 2 - 3 | Notts. County |
| 1986/1987 | F.A. Cup | 2nd Round | Sat 06 Dec | Aldershot | 3 - 2 | Colchester U. |
| League Cup | 1st Round | Wed 03 Sep | Peterborough | 2 - 0 | Colchester U. |
| Peterborough United won 2-0 on aggregate |
| (Associate Members) | Southern 1st Round | Mon 26 Jan | Gillingham | 2 - 0 | Colchester U. |