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Extremadura was founded in 1924, and spent the first 30 years of its existence in the regional leagues, promoting to the second division after winning the regional championship in the third.

The club lasted seven seasons in the category, finishing in fifth position in the 1958–59 season. Subsequently, the following 29 years were spent in the third level – in 1977 it became the fourth, after the creation of Segunda División B – with the addition of three relegations to the regional championships.

In 1990, after finishing first, Extremadura promoted to division three. Four years later, after winning its group, it returned to the second after an absence of 34 years; during that period of time, football in the region of Extremadura experienced a rise, with CD Badajoz and CP Mérida also competing in that level in the mid-1990s.

Extremadura finished in fifth position in the 1995–96 campaign. 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 following year, with a young Rafael Benítez in charge, immediate promotion back was easily attained, as runner-up.

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. The club's financial situation was precarious, and it dropped another division in 2002; in the first season in level three, a fifth position meant a narrow miss in the subsequent promotion playoffs, and the following four years were also spent in the division, with the club never finishing higher than tenth.

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. Shortly afterwards it emerged that the club could not settle its economic problems, with players being due several months in wages. After confirmation by the Royal Spanish Football Federation on 1 August 2008, the club was relegated a further category.

Extremadura's sporting and financial troubles continued in the following years, with the club never ranking higher than 16th. In August 2010 it folded, being dissolved by its major shareholder, the Almendralejo City Hall; that fate had already befallen Mérida, with Badajoz being saved in the last minute, replaced by another team in the city and being dropped to level four.