| Jornada 1 | 31-08-2008 | RAYO VALLEC. | 1 | MURCIA | 0 |
| Jornada 2 | 07-09-2008 | HERCULES | 1 | RAYO VALLEC. | 1 |
| Jornada 3 | 14-09-2008 | RAYO VALLEC. | 2 | ALAVES | 1 |
| Jornada 4 | 21-09-2008 | SEVILLA B | 0 | RAYO VALLEC. | 0 |
| Jornada 5 | 28-09-2008 | RAYO VALLEC. | 3 | XEREZ | 3 |
| Jornada 6 | 05-10-2008 | GIRONA | 1 | RAYO VALLEC. | 1 |
| Jornada 7 | 12-10-2008 | RAYO VALLEC. | 4 | CASTELLON | 2 |
| Jornada 8 | 19-10-2008 | GIMNASTIC | 3 | RAYO VALLEC. | 1 |
| Jornada 9 | 26-10-2008 | RAYO VALLEC. | 4 | EIBAR | 1 |
| Jornada 10 | 02-11-2008 | TENERIFE | 2 | RAYO VALLEC. | 0 |
| Jornada 11 | 09-11-2008 | RAYO VALLEC. | 1 | HUESCA | 0 |
| Jornada 12 | 16-11-2008 | CELTA | 0 | RAYO VALLEC. | 0 |
| Jornada 13 | 23-11-2008 | RAYO VALLEC. | 0 | ALICANTE | 0 |
| Jornada 14 | 30-11-2008 | ALBACETE | 2 | RAYO VALLEC. | 1 |
| Jornada 15 | 07-12-2008 | RAYO VALLEC. | 1 | SALAMANCA | 1 |
| Jornada 16 | 14-12-2008 | CORDOBA | 0 | RAYO VALLEC. | 1 |
| Jornada 17 | 21-12-2008 | ELCHE | 2 | RAYO VALLEC. | 0 |
| Jornada 18 | 04-01-2009 | RAYO VALLEC. | 0 | LEVANTE | 0 |
| Jornada 19 | 11-01-2009 | REAL SOCIEDAD | 1 | RAYO VALLEC. | 1 |
| Jornada 20 | 18-01-2009 | RAYO VALLEC. | 1 | LAS PALMAS | 1 |
| Jornada 21 | 25-01-2009 | ZARAGOZA | 2 | RAYO VALLEC. | 3 |
| Jornada 22 | 01-02-2009 | MURCIA | 0 | RAYO VALLEC. | 1 |
| Jornada 23 | 08-02-2009 | RAYO VALLEC. | 1 | HERCULES | 0 |
| Jornada 24 | 15-02-2009 | ALAVES | 0 | RAYO VALLEC. | 2 |
| Jornada 25 | 22-02-2009 | RAYO VALLEC. | 1 | SEVILLA B | 0 |
| Jornada 26 | 01-03-2009 | XEREZ | 1 | RAYO VALLEC. | 1 |
| Jornada 27 | 08-03-2009 | RAYO VALLEC. | 1 | GIRONA | 1 |
| Jornada 28 | 15-03-2009 | CASTELLON | 0 | RAYO VALLEC. | 0 |
| Jornada 29 | 22-03-2009 | RAYO VALLEC. | 3 | GIMNASTIC | 2 |
| Jornada 30 | 29-03-2009 | EIBAR | 0 | RAYO VALLEC. | 1 |
| Jornada 31 | 05-04-2009 | RAYO VALLEC. | 0 | TENERIFE | 0 |
| Jornada 32 | 12-04-2009 | HUESCA | 0 | RAYO VALLEC. | 1 |
| Jornada 33 | 19-04-2009 | RAYO VALLEC. | 4 | CELTA | 1 |
| Jornada 34 | 26-04-2009 | ALICANTE | 2 | RAYO VALLEC. | 0 |
| Jornada 35 | 03-05-2009 | RAYO VALLEC. | 0 | ALBACETE | 3 |
| Jornada 36 | 10-05-2009 | SALAMANCA | 0 | RAYO VALLEC. | 1 |
| Jornada 37 | 17-05-2009 | RAYO VALLEC. | 5 | CORDOBA | 0 |
| Jornada 38 | 24-05-2009 | RAYO VALLEC. | 1 | ELCHE | 2 |
| Jornada 39 | 31-05-2009 | LEVANTE | 1 | RAYO VALLEC. | 0 |
| Jornada 40 | 07-06-2009 | RAYO VALLEC. | 4 | REAL SOCIEDAD | 1 |
| Jornada 41 | 14-06-2009 | LAS PALMAS | 0 | RAYO VALLEC. | 0 |
| Jornada 42 | 21-06-2009 | RAYO VALLEC. | 2 | ZARAGOZA | 2 |