Peña Deportiva was founded in 1935, but didn't start to compete until 1949. Deportiva only played in the regional leagues until 1985, when the club were promoted to Tercera Division for the first time. Deportiva played there for 8 seasons, before reaching Segunda Division B for the first time in 1993. However, the club lasted one season before they were relegated.
Peña returned to Segunda B in 2008, but they were again relegated after just one season. They remained in Tercera Division until 2017, when they again managed to reach the third tier. However, relegation followed again after the end of the season. Peña promoted again in season 2018-19 and since then are in 2ª RFEF usually playing promotion playoffs.