| League Two | 1 | 2008-08-09 | AWAY | Dagenham Redbridge | 6-0 |
| League Two | 2 | 2008-08-16 | HOME | Wycombe Wanderers | 0-2 |
| League Two | 3 | 2008-08-23 | AWAY | Rotherham United | 3-1 |
| League Two | 4 | 2008-08-30 | HOME | Barnet FC | 5-1 |
| League Two | 5 | 2008-09-06 | HOME | Bury | 1-1 |
| League Two | 6 | 2008-09-13 | AWAY | Grimsby Town | 1-3 |
| League Two | 7 | 2008-09-21 | HOME | Shrewsbury Town | 1-1 |
| League Two | 8 | 2008-09-27 | AWAY | Luton Town | 1-1 |
| League Two | 9 | 2008-10-04 | HOME | Lincoln City | 0-2 |
| League Two | 10 | 2008-10-11 | AWAY | Chesterfield FC | 1-1 |
| League Two | 11 | 2008-10-19 | HOME | Port Vale FC | 1-2 |
| League Two | 12 | 2008-10-21 | AWAY | Rochdale AFC | 6-1 |
| League Two | 13 | 2008-10-25 | AWAY | Gillingham FC | 2-0 |
| League Two | 14 | 2008-10-28 | HOME | Brentford | 3-0 |
| League Two | 15 | 2008-11-01 | AWAY | Exeter City | 2-0 |
| League Two | 16 | 2008-11-15 | HOME | Morecambe FC | 1-2 |
| League Two | 17 | 2008-11-22 | HOME | Aldershot Town | 0-1 |
| League Two | 18 | 2008-11-25 | AWAY | Darlington FC | 1-2 |
| League Two | 19 | 2008-12-06 | AWAY | AFC Bournemouth | 1-0 |
| League Two | 20 | 2008-12-13 | HOME | Notts County | 2-0 |
| League Two | 21 | 2008-12-20 | AWAY | Bradford City | 0-0 |
| League Two | 22 | 2008-12-26 | HOME | Accrington Stanley | 2-0 |
| League Two | 23 | 2008-12-28 | AWAY | Macclesfield Town | 3-1 |
| League Two | 24 | 2009-01-13 | HOME | Luton Town | 2-2 |
| League Two | 26 | 2009-01-17 | HOME | Chesterfield FC | 1-3 |
| League Two | 27 | 2009-01-24 | AWAY | Lincoln City | 1-1 |
| League Two | 28 | 2009-01-27 | AWAY | Port Vale FC | 3-0 |
| League Two | 29 | 2009-01-31 | HOME | Gillingham FC | 0-1 |
| League Two | 30 | 2009-02-03 | HOME | Rochdale AFC | 0-2 |
| League Two | 31 | 2009-02-07 | AWAY | Brentford | 3-0 |
| League Two | 32 | 2009-02-14 | AWAY | Morecambe FC | 3-1 |
| League Two | 25 | 2009-02-17 | AWAY | Shrewsbury Town | 1-0 |
| League Two | 33 | 2009-02-21 | HOME | Exeter City | 0-0 |
| League Two | 34 | 2009-02-28 | HOME | Dagenham Redbridge | 2-2 |
| League Two | 35 | 2009-03-03 | AWAY | Wycombe Wanderers | 2-0 |
| League Two | 36 | 2009-03-07 | AWAY | Barnet FC | 3-1 |
| League Two | 37 | 2009-03-10 | HOME | Rotherham United | 1-5 |
| League Two | 38 | 2009-03-14 | HOME | Grimsby Town | 1-1 |
| League Two | 39 | 2009-03-21 | AWAY | Bury | 1-1 |
| League Two | 40 | 2009-03-28 | HOME | Bradford City | 0-0 |
| League Two | 41 | 2009-04-04 | AWAY | Notts County | 1-2 |
| League Two | 42 | 2009-04-11 | HOME | Macclesfield Town | 0-2 |
| League Two | 43 | 2009-04-13 | AWAY | Accrington Stanley | 0-1 |
| League Two | 44 | 2009-04-18 | HOME | AFC Bournemouth | 0-2 |
| League Two | 45 | 2009-04-25 | AWAY | Aldershot Town | 2-2 |
| League Two | 46 | 2009-05-02 | HOME | Darlington FC | 1-2 |
