One of the oldest clubs in the Valencian Community, Eldense enrolled in the Valencian Football Federation in 1924, and started competing in Tercera División 19 years later. It first appeared in Segunda División in the 1956–57 season, narrowly avoiding relegation after finishing in 16th position; the first spell in that tier lasted three years, in a total of five at the professional level.
On 4 April 2017, Eldense coach Filippo Vito di Pierro and general manager Nobile Capuani were arrested by Spanish authorities on charges of corruption. The detentions occurred after club president David Aguilar made complaints of match fixing following a 0–12 loss to FC Barcelona B, whilst Eldense player Cheikh Saad said that he had seen Aguilar arguing with di Pierro at half-time of the match, calling the latter a "scoundrel"; subsequently, the former asked La Liga president Javier Tebas to investigate those allegations.
Eldense temporarily suspended all sporting activities, also ending its contract with the Italian investment group represented by Capuani. They also released 12 players, with five people being arrested in connection with the events.
