Cartagena was founded on 25 July 1995, in the place of
Club Deportivo Balsicas, due to serious economic problems of the first team of the city,
Cartagena FC, the first president Florentino Manzano was the founder. In the first eight years it was known as
Cartagonova Fútbol Club, and first played in the
third division in the
1998–99 season. The club then changed its name to
Fútbol Club Cartagena and Luis Oliver took over as president, starting his tenure with the club immerse in economic problems and close to relegation. Being saved from folding by local entrepreneur Francisco Gómez after
the 2002–03 campaign, it consolidated itself in the third level and achieved another
promotion, now to
division two, in
2009. Historic side
Cartagena FC, which was founded much earlier, acted as
reserve team between 2003 and 2009, eventually re-gaining its independence. In
2009–10's second division season Efesé nearly achieved another promotion, finishing eventually in fifth position; all promotion hopes were dashed in the 41st and penultimate matchday, with a 0–1 away loss against
Recreativo de Huelva. Cartagena was relegated from the second tier at the end of
2011–12. In May 2015, a late goal from
Carlos Martínez saved the club from a further drop by winning a
play-off on the
away goals rule against
Las Palmas Atlético.
Three years later, the team fell at the final promotion hurdle to
Extremadura UD by a single goal. On 19 July 2020, Cartagena was promoted to Segunda Division after an 8-year absence. On 13 April 2025, Cartagena was relegated to third division after five years stay in second division following a 1-2 defeated by
Almería. ==Season to season==