The club is considered a continuation of the Cartagena club, founded in 1919.
Cartagena was founded on July 25, 1995 on the site of the Deportivo Balsicas club due to serious economic problems of the city's first team, Cartagena, whose founder was the first president, Florentino Manzano.
For the first eight years it was known as Cartagonova Football Club and played in the third division for the first time in the 1998–99 season.
The club then changed its name to Cartagena Football Club and Luis Oliver took over as president, beginning his term with the club plunged into economic troubles and close to relegation.
Having been rescued from the fold by local entrepreneur Francisco Gomez after the 2002–03 campaign, they established themselves in the third tier and achieved another promotion in 2009, now to the second division.
The historic Cartagena club, founded much earlier, played as a reserve team between 2003 and 2009, eventually regaining independence.
In the 2009–10 season in the second division, Efes almost achieved another promotion, eventually finishing in fifth place;
All hopes of promotion were dashed in the 41st and penultimate matchday when the team lost 0–1 away to Recreativo de Huelva.