Key: Win : Draw : Loss
| Date | Home | Away | Ref | ||
|---|---|---|---|---|---|
| 08/08/2009 | Gillingham | 5 | 0 | Swindon | G Horwood |
| 15/08/2009 | Tranmere | 4 | 2 | Gillingham | C Pawson |
| 18/08/2009 | Colchester | 2 | 1 | Gillingham | G Hegley |
| 22/08/2009 | Gillingham | 0 | 1 | Hartlepool | D McDermid |
| 29/08/2009 | Walsall | 0 | 0 | Gillingham | K Evans |
| 05/09/2009 | Gillingham | 3 | 0 | Exeter | S Hooper |
| 12/09/2009 | Gillingham | 2 | 0 | Millwall | K Stroud |
| 19/09/2009 | Leeds | 4 | 1 | Gillingham | G Salisbury |
| 26/09/2009 | Gillingham | 1 | 1 | Norwich | P Taylor |
| 03/10/2009 | Southampton | 4 | 1 | Gillingham | S Attwell |
| 10/10/2009 | Gillingham | 3 | 2 | Wycombe | P Crossley |
| 13/10/2009 | Brighton | 2 | 0 | Gillingham | G Scott |
| 17/10/2009 | Milton Keynes Dons | 2 | 0 | Gillingham | P Gibbs |
| 24/10/2009 | Gillingham | 1 | 1 | Charlton | J Moss |
| 30/10/2009 | Southend | 1 | 0 | Gillingham | G Ward |
| 14/11/2009 | Gillingham | 1 | 0 | Oldham | M Russell |
| 21/11/2009 | Bristol Rvs | 2 | 1 | Gillingham | K Evans |
| 24/11/2009 | Gillingham | 1 | 0 | Yeovil | P Miller |
| 01/12/2009 | Leyton Orient | 3 | 1 | Gillingham | A D'Urso |
| 05/12/2009 | Gillingham | 0 | 0 | Carlisle | J Singh |
| 12/12/2009 | Huddersfield | 2 | 1 | Gillingham | G Eltringham |
| 19/12/2009 | Gillingham | 3 | 1 | Stockport | D Phillips |
| 26/12/2009 | Gillingham | 0 | 1 | Brentford | F Graham |
| 28/12/2009 | Exeter | 1 | 1 | Gillingham | S Bratt |
| 16/01/2010 | Swindon | 3 | 1 | Gillingham | S Tanner |
| 23/01/2010 | Gillingham | 0 | 0 | Colchester | O Langford |
| 26/01/2010 | Hartlepool | 1 | 1 | Gillingham | K Hill |
| 30/01/2010 | Gillingham | 0 | 0 | Walsall | D Deadman |
| 06/02/2010 | Brentford | 4 | 0 | Gillingham | P Miller |
| 09/02/2010 | Gillingham | 0 | 1 | Tranmere | R East |
| 13/02/2010 | Yeovil | 0 | 0 | Gillingham | P Crossley |
| 20/02/2010 | Gillingham | 1 | 0 | Bristol Rvs | D McDermid |
| 23/02/2010 | Gillingham | 1 | 1 | Leyton Orient | D Sheldrake |
| 27/02/2010 | Carlisle | 2 | 0 | Gillingham | P Tierney |
| 06/03/2010 | Gillingham | 2 | 0 | Huddersfield | F Graham |
| 13/03/2010 | Stockport | 0 | 0 | Gillingham | D Foster |
| 20/03/2010 | Charlton | 2 | 2 | Gillingham | P Taylor |
| 27/03/2010 | Gillingham | 2 | 2 | Milton Keynes Dons | P Crossley |
| 03/04/2010 | Oldham | 1 | 0 | Gillingham | C Boyeson |
| 05/04/2010 | Gillingham | 3 | 0 | Southend | G Scott |
| 10/04/2010 | Millwall | 4 | 0 | Gillingham | M Haywood |
| 13/04/2010 | Gillingham | 1 | 1 | Brighton | J Linington |
| 17/04/2010 | Gillingham | 3 | 2 | Leeds | A Wiley |
| 24/04/2010 | Norwich | 2 | 0 | Gillingham | T Kettle |
| 01/05/2010 | Gillingham | 2 | 1 | Southampton | M Russell |
| 08/05/2010 | Wycombe | 3 | 0 | Gillingham | P Taylor |