| 4. Round | 22/08/2008 | Stade de Reims | - | Montpellier HSC | 0:4 | ||||
| 5. Round | 01/09/2008 | Montpellier HSC | - | FC Metz | 1:2 | ||||
| 6. Round | 12/09/2008 | Dijon FCO | - | Montpellier HSC | 1:0 | ||||
| 7. Round | 19/09/2008 | Montpellier HSC | - | CS Sedan | 3:1 | ||||
| 8. Round | 27/09/2008 | LB Châteauroux | - | Montpellier HSC | 1:1 |  |
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| 9. Round | 03/10/2008 | Montpellier HSC | - | SC Bastia | 2:1 | ||||
| 10. Round | 10/10/2008 | Stade Brestois 29 | - | Montpellier HSC | 0:3 | ||||
| 11. Round | 17/10/2008 | Montpellier HSC | - | Vannes OC | 3:1 | ||||
| 12. Round | 24/10/2008 | Clermont Foot Auvergne 63 | - | Montpellier HSC | 2:1 | |
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| 13. Round | 31/10/2008 | Montpellier HSC | - | Nîmes Olympique | 1:1 | ||||
| 21. Round | 02/02/2009 | US Boulogne | - | Montpellier HSC | 0:3 | |
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| 23. Round | 13/02/2009 | FC Metz | - | Montpellier HSC | 3:1 | ||||
| 24. Round | 20/02/2009 | Montpellier HSC | - | Dijon FCO | 4:1 | ||||
| 25. Round | 27/02/2009 | CS Sedan | - | Montpellier HSC | 1:1 | ||||
| 26. Round | 06/03/2009 | Montpellier HSC | - | LB Châteauroux | 3:0 | ||||
| 27. Round | 13/03/2009 | SC Bastia | - | Montpellier HSC | 1:0 | |
France