However, Real Madrid Castilla was ineligible for the playoffs, and Extremadura took its place, achieving promotion to La Liga for the first time ever after disposing of Albacete Balompié 2–0 on aggregate – Iosu Ortoundo was the manager.

The first season in the top flight was difficult as expected: the team lost its first nine matches and only won one of the first 19, but eventually recovered, finishing only one point from the safety zone.

In the 1998–99 season Extremadura finished in 17th position, and the second top flight campaign also ended in relegation, after losing in the playoffs against Rayo Vallecano.

After the regular season in 2006–07, Extremadura faced UD Pájara Playas de Jandía from the island of Fuerteventura in the relegation playoffs: after a 0–3 away loss, a 1–1 home draw returned the club to the fourth division, after 17 years.

On 12 October 1951, Extremadura played Sevilla FC in the inaugural match at the new grounds, Estadio Francisco de la Hera.