Founded in 1975,[1] Penya Independent played in the regional leagues until 2014, when the club became inactive.

Back to action in 2019, the club played two seasons in the Regional Preferente before winning the Copa del Rey play-offs in 2021, subsequently qualifying to the preliminary rounds of the 2021–22 Copa del Rey;[4] they were knocked out by CFJ Mollerussa, however.

On 19 June 2022, Penya Independent achieved a first-ever promotion to Tercera Federación, after defeating SCR Peña Deportiva's reserve team.

[5] On 4 June 2023, Penya Independent achieved his second successive promotion defeating Ejea after extra time in the 2023 Tercera Federación play-offs after finishing in third position in regular league.

[6][7] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.