One of the oldest clubs in the Valencian Community, Eldense joined the Valencian Football Federation in 1924 and began competing in the Tercera Division 19 years later.
He made his first Segunda appearance in the 1956–57 season, narrowly avoiding relegation after finishing in 16th place;
On April 4, 2017, Eldense coach Filippo Vito di Piero and general manager Nobile Capuani were arrested by Spanish authorities on corruption charges.
The arrests came after club president David Aguilar complained about match-fixing following a 0-12 defeat to Barcelona B, while Eldense player Sheikh Saad said he saw Aguilar arguing with Di Piero at half-time
"scoundrel";
Eldense temporarily suspended all sports activities and also terminated its contract with the Italian investment group represented by Capuani.
They also released 12 players and five people were arrested in connection with the events.
Eldense spent four years in Tercera División and was relegated to the new fourth-tier RFEF Segunda División for the 2020–21 season due to a restructuring of the Spanish football league system.
On 28 May 2022, Eldense secured a second consecutive promotion to the new third-tier Primera Federación after defeating Sestao River in the last play-off match.
On 25 June 2023, Eldense achieved promotion to the Segunda Division after a draw with Real Madrid Castilla.
The play-offs ended 4–4 on aggregate, meaning Eldens were promoted thanks to a better regular season finish.
Eldens returned to the second tier after a 59-year absence and achieved three promotions in a row.