| Colchester Royals | | 1993 | | First Round | 19-09-1993 | | Welwyn Garden City | Colchester Royals | 1-10 | | Second Round | 17-10-1993 | | Colchester Royals | St Germaine | 2-6 | | 1994 | | Second Round | 16-10-1994 | | Colchester Royals | Pagham | 3-1 | | Third Round | 13-11-1994 | | Enfield | Colchester Royals | 6-1 | | 1995 | | First Round | 17-09-1995 | | Edenbridge Town | Colchester Royals | 3-4 | | Second Round | 15-10-1995 | | Mill Hill United | Colchester Royals | 4-2 | | Colchester United | | 2002 | | First Round | 03-11-2002 | | Colchester United | Westbourne | 4-0 | | Second Round | 17-11-2002 | | Reading Royals | Colchester United | 8-1 | | 2003 | | First Round | 26-10-2003 | | Colchester United | Barking | 2-0 | | Second Round | 09-11-2003 | | Leyton Orient | Colchester United | 3-1 | | 2004 | | 1st Qualifying Round | 05-09-2004 | | Colchester United | Ruschliffe | 13-0 | | 2nd Qualifying Round | 26-09-2004 | | Walsall | Colchester United | 2-7 | | First Round | 24-10-2004 | | Colchester United | TNS | 2-1 | | Second Round | 21-11-2004 | | Norwich City | Colchester United | 4-3 | | 2005 | | First Round | 23-10-2005 | | Colchester United | Dynamo North London | 7-0 | | Second Round | 13-11-2005 | | Gravesend & Northfleet | Colchester United | 0-1 | | Third Round | 04-12-2005 | | Colchester United | Staines Town | 3-2 | | Fourth Round | 08-01-2006 | | Liverpool | Colchester United | 1-0 | |
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| 2006 | | First Round | 29-10-2006 | | Oxford City | Colchester United | 1-6 | | Second Round | 12-11-2006 | | Colchester United | Gillingham | 7-2 | | Third Round | 10-12-2006 | | Colchester United | Bedford Town Bells | 3-2 | | Fourth Round | 14-01-2007 | | Aston Villa | Colchester United | 0-1 | | Fifth Round | 28-01-2007 | | Colchester United | Birmingham City | 0-5 | |
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| 2007 | | Third Round | 16-12-2007 | | Colchester United | Luton Town | 3-1 | | Fourth Round | 06-01-2008 | | West Ham United | Colchester United | 7-0 | | 2008 | | Third Round | 21-12-2008 | | Enfield Town | Colchester United | 0-1 | | Fourth Round | 11-01-2009 | | Arsenal | Colchester United | 7-0 | | 2009 | | Third Round | 13-12-2009 | | Colchester United | East Preston | 4-0 | | Fourth Round | 24-01-2010 | | Colchester United | Barnet | 2-3 | |
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| 2010 | | Second Round | 16-01-2011 | | Tottenham Hotspur | Colchester United | 1-2 | | Third Round | 06-02-2011 | | Colchester United | Newcastle United | 2-1 | | Fourth Round | 06-03-2011 | | West Ham United | Colchester United | 4-2 | | 2011 | | Second Round | 08-01-2012 | | Gillingham | Colchester United | 3-0 | | 2012 | | Second Round | 06-01-2013 | | Colchester United | Sporting Club Albion | 1-5 |
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