Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 08/08/2009 | Southend | 2 | 2 | Huddersfield | S Cook |
| 15/08/2009 | Walsall | 2 | 2 | Southend | J Moss |
| 18/08/2009 | Wycombe | 1 | 1 | Southend | J Linington |
| 21/08/2009 | Southend | 0 | 0 | Millwall | D Whitestone |
| 29/08/2009 | Swindon | 2 | 1 | Southend | M Russell |
| 04/09/2009 | Southend | 3 | 0 | Leyton Orient | T Kettle |
| 11/09/2009 | Southend | 0 | 0 | Leeds | P Taylor |
| 19/09/2009 | Brighton | 2 | 3 | Southend | R East |
| 26/09/2009 | Southend | 0 | 1 | Oldham | K Hill |
| 29/09/2009 | Brentford | 2 | 1 | Southend | K Wright |
| 03/10/2009 | Stockport | 0 | 2 | Southend | S Bratt |
| 09/10/2009 | Southend | 1 | 3 | Southampton | G Hegley |
| 17/10/2009 | Southend | 2 | 1 | Bristol Rvs | C Pawson |
| 24/10/2009 | Carlisle | 2 | 1 | Southend | G Eltringham |
| 30/10/2009 | Southend | 1 | 0 | Gillingham | G Ward |
| 14/11/2009 | Yeovil | 1 | 0 | Southend | D Phillips |
| 20/11/2009 | Southend | 2 | 1 | Milton Keynes Dons | D Deadman |
| 24/11/2009 | Tranmere | 2 | 0 | Southend | D Webb |
| 01/12/2009 | Southend | 0 | 3 | Norwich | P Crossley |
| 05/12/2009 | Charlton | 1 | 0 | Southend | D McDermid |
| 12/12/2009 | Southend | 3 | 2 | Hartlepool | P Gibbs |
| 19/12/2009 | Exeter | 1 | 0 | Southend | R East |
| 26/12/2009 | Southend | 1 | 2 | Colchester | G Hegley |
| 28/12/2009 | Leyton Orient | 1 | 2 | Southend | G Ward |
| 16/01/2010 | Huddersfield | 2 | 1 | Southend | E Ilderton |
| 23/01/2010 | Southend | 1 | 1 | Wycombe | D Whitestone |
| 26/01/2010 | Millwall | 2 | 0 | Southend | K Evans |
| 30/01/2010 | Southend | 2 | 2 | Swindon | D Phillips |
| 08/02/2010 | Colchester | 2 | 0 | Southend | N Miller |
| 13/02/2010 | Southend | 1 | 1 | Tranmere | S Cook |
| 20/02/2010 | Milton Keynes Dons | 3 | 1 | Southend | L Mason |
| 23/02/2010 | Norwich | 2 | 1 | Southend | M Russell |
| 26/02/2010 | Southend | 1 | 2 | Charlton | K Wright |
| 06/03/2010 | Hartlepool | 3 | 0 | Southend | J Waugh |
| 13/03/2010 | Southend | 0 | 0 | Exeter | D Sheldrake |
| 20/03/2010 | Southend | 2 | 2 | Carlisle | A Woolmer |
| 23/03/2010 | Southend | 3 | 0 | Walsall | C Boyeson |
| 27/03/2010 | Bristol Rvs | 4 | 3 | Southend | S Rushton |
| 03/04/2010 | Southend | 0 | 0 | Yeovil | R Booth |
| 05/04/2010 | Gillingham | 3 | 0 | Southend | G Scott |
| 10/04/2010 | Leeds | 2 | 0 | Southend | E Ilderton |
| 13/04/2010 | Southend | 2 | 2 | Brentford | T Kettle |
| 17/04/2010 | Southend | 0 | 1 | Brighton | S Hooper |
| 24/04/2010 | Oldham | 2 | 2 | Southend | S Tanner |
| 01/05/2010 | Southend | 2 | 1 | Stockport | C Sarginson |
| 08/05/2010 | Southampton | 3 | 1 | Southend | R Shoebridge |