Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 08/08/2009 | Oldham | 0 | 0 | Stockport | O Langford |
| 15/08/2009 | Stockport | 0 | 2 | Bristol Rvs | D Webb |
| 18/08/2009 | Stockport | 1 | 2 | Carlisle | A Hall |
| 22/08/2009 | Brighton | 2 | 4 | Stockport | S Cook |
| 29/08/2009 | Stockport | 1 | 1 | Southampton | C Boyeson |
| 05/09/2009 | Leeds | 2 | 0 | Stockport | D McDermid |
| 12/09/2009 | Yeovil | 2 | 2 | Stockport | G Scott |
| 19/09/2009 | Stockport | 2 | 1 | Leyton Orient | A Haines |
| 26/09/2009 | Huddersfield | 0 | 0 | Stockport | O Langford |
| 29/09/2009 | Stockport | 2 | 2 | Hartlepool | C Sarginson |
| 03/10/2009 | Stockport | 0 | 2 | Southend | S Bratt |
| 12/10/2009 | Tranmere | 0 | 1 | Stockport | R Booth |
| 17/10/2009 | Stockport | 0 | 4 | Millwall | M Haywood |
| 24/10/2009 | Brentford | 2 | 0 | Stockport | G Ward |
| 31/10/2009 | Stockport | 1 | 3 | Norwich | A Woolmer |
| 14/11/2009 | Walsall | 2 | 0 | Stockport | S Rushton |
| 21/11/2009 | Stockport | 1 | 3 | Exeter | M Jones |
| 24/11/2009 | Colchester | 2 | 0 | Stockport | P Gibbs |
| 05/12/2009 | Wycombe | 2 | 1 | Stockport | D Sheldrake |
| 12/12/2009 | Stockport | 1 | 2 | Charlton | E Ilderton |
| 19/12/2009 | Gillingham | 3 | 1 | Stockport | D Phillips |
| 26/12/2009 | Milton Keynes Dons | 4 | 1 | Stockport | T Kettle |
| 28/12/2009 | Stockport | 2 | 4 | Leeds | K Friend |
| 19/01/2010 | Stockport | 0 | 1 | Swindon | G Salisbury |
| 23/01/2010 | Carlisle | 0 | 0 | Stockport | C Sarginson |
| 26/01/2010 | Stockport | 1 | 1 | Brighton | P Quinn |
| 30/01/2010 | Southampton | 2 | 0 | Stockport | F Graham |
| 06/02/2010 | Stockport | 1 | 3 | Milton Keynes Dons | J Waugh |
| 13/02/2010 | Stockport | 2 | 2 | Colchester | A Haines |
| 20/02/2010 | Exeter | 0 | 1 | Stockport | G Ward |
| 23/02/2010 | Swindon | 4 | 1 | Stockport | R East |
| 27/02/2010 | Stockport | 4 | 3 | Wycombe | C Webster |
| 02/03/2010 | Bristol Rvs | 1 | 0 | Stockport | D Whitestone |
| 06/03/2010 | Charlton | 2 | 0 | Stockport | K Stroud |
| 13/03/2010 | Stockport | 0 | 0 | Gillingham | D Foster |
| 16/03/2010 | Stockport | 0 | 1 | Oldham | J Moss |
| 20/03/2010 | Stockport | 0 | 1 | Brentford | N Miller |
| 27/03/2010 | Millwall | 5 | 0 | Stockport | P Miller |
| 03/04/2010 | Stockport | 1 | 1 | Walsall | M Oliver |
| 05/04/2010 | Norwich | 2 | 1 | Stockport | F Graham |
| 10/04/2010 | Stockport | 1 | 3 | Yeovil | G Eltrigham |
| 13/04/2010 | Hartlepool | 3 | 0 | Stockport | A Hall |
| 17/04/2010 | Leyton Orient | 2 | 0 | Stockport | S Rushton |
| 24/04/2010 | Stockport | 0 | 6 | Huddersfield | A Woolmer |
| 01/05/2010 | Southend | 2 | 1 | Stockport | C Sarginson |
| 08/05/2010 | Stockport | 0 | 3 | Tranmere | T Kettle |