| Jornada 1 | 31-08-2008 | OSASUNA | 1 | VILLARREAL | 1 |
| Jornada 2 | 14-09-2008 | VILLARREAL | 1 | DEPORTIVO | 0 |
| Jornada 3 | 21-09-2008 | NUMANCIA | 1 | VILLARREAL | 2 |
| Jornada 4 | 24-09-2008 | VILLARREAL | 2 | RAC.SANTANDER | 0 |
| Jornada 5 | 28-09-2008 | SPORTING GIJON | 0 | VILLARREAL | 1 |
| Jornada 6 | 05-10-2008 | VILLARREAL | 2 | BETIS | 1 |
| Jornada 7 | 19-10-2008 | ESPANYOL | 0 | VILLARREAL | 0 |
| Jornada 8 | 26-10-2008 | VILLARREAL | 4 | ATLETICO MADRID | 4 |
| Jornada 9 | 02-11-2008 | ATHLETIC BILBAO | 1 | VILLARREAL | 4 |
| Jornada 10 | 09-11-2008 | VILLARREAL | 2 | ALMERIA | 1 |
| Jornada 11 | 16-11-2008 | MALAGA | 2 | VILLARREAL | 2 |
| Jornada 12 | 23-11-2008 | VILLARREAL | 0 | VALLADOLID | 3 |
| Jornada 13 | 30-11-2008 | RECREATIVO | 1 | VILLARREAL | 2 |
| Jornada 14 | 07-12-2008 | VILLARREAL | 3 | GETAFE | 3 |
| Jornada 15 | 14-12-2008 | SEVILLA | 1 | VILLARREAL | 0 |
| Jornada 16 | 21-12-2008 | VILLARREAL | 1 | FC BARCELONA | 2 |
| Jornada 17 | 04-01-2009 | REAL MADRID | 1 | VILLARREAL | 0 |
| Jornada 18 | 11-01-2009 | VALENCIA | 3 | VILLARREAL | 3 |
| Jornada 19 | 18-01-2009 | VILLARREAL | 2 | MALLORCA | 0 |
| Jornada 20 | 25-01-2009 | VILLARREAL | 1 | OSASUNA | 1 |
| Jornada 21 | 01-02-2009 | DEPORTIVO | 3 | VILLARREAL | 0 |
| Jornada 22 | 08-02-2009 | VILLARREAL | 2 | NUMANCIA | 1 |
| Jornada 23 | 15-02-2009 | RAC.SANTANDER | 1 | VILLARREAL | 1 |
| Jornada 24 | 22-02-2009 | VILLARREAL | 2 | SPORTING GIJON | 1 |
| Jornada 25 | 01-03-2009 | BETIS | 2 | VILLARREAL | 2 |
| Jornada 26 | 08-03-2009 | VILLARREAL | 1 | ESPANYOL | 0 |
| Jornada 27 | 15-03-2009 | ATLETICO MADRID | 3 | VILLARREAL | 2 |
| Jornada 28 | 22-03-2009 | VILLARREAL | 2 | ATHLETIC BILBAO | 0 |
| Jornada 29 | 05-04-2009 | ALMERIA | 3 | VILLARREAL | 0 |
| Jornada 30 | 12-04-2009 | VILLARREAL | 0 | MALAGA | 2 |
| Jornada 31 | 19-04-2009 | VALLADOLID | 0 | VILLARREAL | 0 |
| Jornada 32 | 22-04-2009 | VILLARREAL | 2 | RECREATIVO | 1 |
| Jornada 33 | 26-04-2009 | GETAFE | 1 | VILLARREAL | 2 |
| Jornada 34 | 03-05-2009 | VILLARREAL | 0 | SEVILLA | 2 |
| Jornada 35 | 10-05-2009 | FC BARCELONA | 3 | VILLARREAL | 3 |
| Jornada 36 | 17-05-2009 | VILLARREAL | 3 | REAL MADRID | 2 |
| Jornada 37 | 24-05-2009 | VILLARREAL | 3 | VALENCIA | 1 |
| Jornada 38 | 31-05-2009 | MALLORCA | 2 | VILLARREAL | 3 |