Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 06/08/2011 | Preston | 2 | 4 | Colchester | C Pawson |
| 13/08/2011 | Colchester | 1 | 1 | Wycombe | G Sutton |
| 16/08/2011 | Colchester | 0 | 2 | Charlton | O Langford |
| 20/08/2011 | Huddersfield | 3 | 2 | Colchester | I Williamson |
| 27/08/2011 | Colchester | 4 | 1 | Oldham | S Rushton |
| 03/09/2011 | Scunthorpe | 1 | 1 | Colchester | N Miller |
| 10/09/2011 | Colchester | 1 | 1 | Leyton Orient | A D'Urso |
| 13/09/2011 | Brentford | 1 | 1 | Colchester | G Ward |
| 17/09/2011 | Sheffield United | 3 | 0 | Colchester | D Deadman |
| 24/09/2011 | Colchester | 1 | 0 | Walsall | S Hooper |
| 01/10/2011 | Chesterfield | 0 | 1 | Colchester | D Mohareb |
| 08/10/2011 | Colchester | 2 | 2 | Yeovil | C Sarginson |
| 15/10/2011 | Rochdale | 2 | 2 | Colchester | D Webb |
| 22/10/2011 | Sheffield Weds | 2 | 0 | Colchester | G Eltringham |
| 25/10/2011 | Colchester | 1 | 1 | Bournemouth | J Waugh |
| 29/10/2011 | Colchester | 4 | 2 | Notts County | G Scott |
| 05/11/2011 | Tranmere | 0 | 0 | Colchester | G Salisbury |
| 19/11/2011 | Colchester | 1 | 5 | Milton Keynes Dons | B Malone |
| 26/11/2011 | Carlisle | 1 | 0 | Colchester | M Heywood |
| 10/12/2011 | Colchester | 4 | 1 | Bury | J Adcock |
| 17/12/2011 | Hartlepool | 0 | 1 | Colchester | E Ilderton |
| 26/12/2011 | Colchester | 1 | 6 | Stevenage | F Graham |
| 31/12/2011 | Colchester | 2 | 0 | Exeter | P Gibbs |
| 02/01/2012 | Milton Keynes Dons | 1 | 0 | Colchester | C Berry |
| 14/01/2012 | Colchester | 1 | 1 | Scunthorpe | D Phillips |
| 21/01/2012 | Colchester | 1 | 2 | Chesterfield | M Brown |
| 28/01/2012 | Leyton Orient | 0 | 1 | Colchester | M Haywood |
| 14/02/2012 | Colchester | 2 | 1 | Brentford | J Linington |
| 18/02/2012 | Yeovil | 3 | 2 | Colchester | S Rushton |
| 25/02/2012 | Colchester | 0 | 0 | Rochdale | D Coote |
| 28/02/2012 | Oldham | 1 | 1 | Colchester | O Langford |
| 03/03/2012 | Colchester | 3 | 0 | Preston | L Collins |
| 06/03/2012 | Charlton | 0 | 2 | Colchester | G Ward |
| 10/03/2012 | Wycombe | 0 | 0 | Colchester | S Hooper |
| 13/03/2012 | Colchester | 1 | 1 | Sheffield United | T Kettle |
| 17/03/2012 | Colchester | 1 | 1 | Huddersfield | D Mohareb |
| 20/03/2012 | Stevenage | 0 | 0 | Colchester | D Deadman |
| 24/03/2012 | Colchester | 1 | 1 | Carlisle | G Sutton |
| 27/03/2012 | Walsall | 3 | 1 | Colchester | R Lewis |
| 31/03/2012 | Exeter | 1 | 1 | Colchester | D Drysdale |
| 06/04/2012 | Colchester | 1 | 1 | Hartlepool | P Miller |
| 09/04/2012 | Bury | 4 | 1 | Colchester | G Eltringham |
| 14/04/2012 | Colchester | 1 | 1 | Sheffield Weds | C Boyeson |
| 21/04/2012 | Bournemouth | 1 | 1 | Colchester | S Attwell |
| 28/04/2012 | Colchester | 4 | 2 | Tranmere | A Haines |
| 05/05/2012 | Notts County | 4 | 1 | Colchester | S Mathieson |