| R | Date | Home | Score | Away | HT | Crowd | >2.5 | HT | FT | TV | Time | Rating | Ref. | Location | |
| 1 | 05.08.2006 | Birmingham City | 2 - 1 | Colchester Utd | 1-0 | 24'238 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 2 | 08.08.2006 | Colchester Utd | 0 - 1 | Plymouth Argyle | 0-1 | 4'627 | No | 2 | 2 | 19:45 | 0 | 0 | |||
| 3 | 12.08.2006 | Colchester Utd | 1 - 2 | Barnsley | 1-0 | 4'249 | Yes | 1 | 2 | 15:00 | 0 | 0 | |||
| 4 | 19.08.2006 | West Brom | 2 - 1 | Colchester Utd | 2-0 | 17'509 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 5 | 26.08.2006 | Colchester Utd | 4 - 3 | Derby County | 2-1 | 4'574 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 6 | 09.09.2006 | Burnley | 1 - 2 | Colchester Utd | 0-1 | 10'039 | Yes | 2 | 2 | 15:00 | 0 | 0 | |||
| 7 | 12.09.2006 | Luton Town | 1 - 1 | Colchester Utd | 1-1 | 7'609 | No | X | X | 19:45 | 0 | 0 | |||
| 8 | 16.09.2006 | Colchester Utd | 2 - 1 | QPR | 2-0 | 5'246 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 9 | 23.09.2006 | Leicester City | 0 - 0 | Colchester Utd | 0-0 | 22'449 | No | X | X | 15:00 | 0 | 0 | |||
| 10 | 29.09.2006 | Colchester Utd | 1 - 0 | Ipswich Town | 1-0 | 6'065 | No | 1 | 1 | 19:45 | 0 | 0 | |||
| 11 | 14.10.2006 | Wolves | 1 - 0 | Colchester Utd | 0-0 | 19'318 | No | X | 1 | 15:00 | 0 | 0 | |||
| 12 | 18.10.2006 | Colchester Utd | 4 - 0 | Sheffield Wed | 1-0 | 5'097 | Yes | 1 | 1 | 19:45 | 0 | 0 | |||
| 13 | 23.10.2006 | Coventry City | 2 - 1 | Colchester Utd | 1-0 | 16'178 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 14 | 28.10.2006 | Colchester Utd | 2 - 0 | Southampton | 1-0 | 5'893 | No | 1 | 1 | 15:00 | 0 | 0 | |||
| 15 | 31.10.2006 | Norwich City | 1 - 1 | Colchester Utd | 0-0 | 25'065 | No | X | X | 19:45 | 0 | 0 | |||
| 16 | 04.11.2006 | Colchester Utd | 3 - 1 | Cardiff City | 0-0 | 5'393 | Yes | X | 1 | 15:00 | 0 | 0 | |||
| 17 | 11.11.2006 | Leeds United | 3 - 0 | Colchester Utd | 1-0 | 17'678 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 18 | 18.11.2006 | Sunderland | 3 - 1 | Colchester Utd | 1-0 | 25'197 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 19 | 25.11.2006 | Colchester Utd | 3 - 0 | Southend Utd | 0-0 | 5'954 | Yes | X | 1 | 15:00 | 0 | 0 | |||
| 20 | 28.11.2006 | Colchester Utd | 5 - 1 | Hull City | 1-1 | 5'373 | Yes | X | 1 | 19:45 | 0 | 0 | |||
| 21 | 02.12.2006 | Cardiff City | 0 - 0 | Colchester Utd | 0-0 | 13'512 | No | X | X | 15:00 | 0 | 0 | |||
| 22 | 09.12.2006 | Crystal Pal. | 1 - 3 | Colchester Utd | 0-0 | 16'762 | Yes | X | 2 | 15:00 | 0 | 0 | |||
| 23 | 16.12.2006 | Colchester Utd | 3 - 0 | Stoke City | 2-0 | 5'345 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 24 | 23.12.2006 | Preston | 1 - 0 | Colchester Utd | 1-0 | 14'225 | No | 1 | 1 | 15:00 | 0 | 0 | |||
| 25 | 26.12.2006 | Colchester Utd | 4 - 1 | Luton Town | 2-0 | 5'427 | Yes | 1 | 1 | 15:00 | 0 | 0 | |||
| 26 | 30.12.2006 | Colchester Utd | 2 - 1 | Wolves | 0-0 | Yes | X | 1 | 15:00 | 0 | 0 | ||||
| 27 | 01.01.2007 | QPR | 1 - 0 | Colchester Utd | 0-0 | No | X | 1 | 15:00 | 0 | 0 | ||||
| 28 | 13.01.2007 | Colchester Utd | 1 - 1 | Leicester City | 0-0 | No | X | X | 15:00 | 0 | 0 | ||||
| 29 | 20.01.2007 | Ipswich Town | 3 - 2 | Colchester Utd | 0-0 | Yes | X | 1 | 15:00 | 0 | 0 | ||||
| 30 | 30.01.2007 | Colchester Utd | 1 - 0 | Preston | 0-0 | No | X | 1 | 19:45 | 0 | 0 | ||||
| 31 | 03.02.2007 | Colchester Utd | 1 - 1 | Birmingham City | 0-0 | No | X | X | 15:00 | 0 | 0 | ||||
| 32 | 10.02.2007 | Barnsley | 0 - 3 | Colchester Utd | 0-0 | Yes | X | 2 | 15:00 | 0 | 0 | ||||
| 33 | 13.02.2007 | Colchester Utd | 1 - 2 | West Brom | 0-0 | Yes | X | 2 | 15:00 | 0 | 0 | ||||
| 34 | 20.02.2007 | Plymouth Argyle | 3 - 0 | Colchester Utd | 0-0 | Yes | X | 1 | 19:45 | 0 | 0 | ||||
| 35 | 24.02.2007 | Colchester Utd | 0 - 0 | Burnley | 0-0 | No | X | X | 15:00 | 0 | 0 | ||||
| 36 | 02.03.2007 | Derby County | 5 - 1 | Colchester Utd | 0-0 | Yes | X | 1 | 15:00 | 0 | 0 | ||||
| 37 | 10.03.2007 | Colchester Utd | - | Coventry City | 15:00 | ||||||||||
| 38 | 13.03.2007 | Sheffield Wed | - | Colchester Utd | 19:45 | ||||||||||
| 39 | 16.03.2007 | Southampton | - | Colchester Utd | 15:00 | ||||||||||
| 40 | 31.03.2007 | Colchester Utd | - | Norwich City | 15:00 | ||||||||||
| 41 | 06.04.2007 | Southend Utd | - | Colchester Utd | 12:00 | ||||||||||
| 42 | 09.04.2007 | Colchester Utd | - | Leeds United | 15:00 | ||||||||||
| 43 | 14.04.2007 | Hull City | - | Colchester Utd | 15:00 | ||||||||||
| 44 | 21.04.2007 | Colchester Utd | - | Sunderland | 15:00 | ||||||||||
| 45 | 28.04.2007 | Stoke City | - | Colchester Utd | 15:00 | ||||||||||
| 46 | 06.05.2007 | Colchester Utd | - | Crystal Pal. | 15:00 |