El Nacional was founded on 1 June 1964, and was administered by the Ecuadorian Military since the foundation until 2013, when the club celebrated its first democratic elections.

The club has maintained a tradition of only playing Ecuadorian footballers,[3] which has given them the nickname of Puros Criollos ("Pure Natives").

Fabián Paz y Miño stepped up as the leading goal scorer in the league in 1977 to help El Nacional during those three years of glory.

El Nacional produced some of the greatest players in Ecuador and won two more championships in 1992 and 1996 with the help of Cléber Chalá, Agustín Delgado, and Oswaldo Ibarra.

El Nacional has brought up talented players such as Antonio Valencia, Segundo Alejandro Castillo, Christian Benítez and Felix Borja.

On 13 May 1998, a group of friends met and decided to form a highly dedicated fanbase called La Marea Roja (English: The Red Tide).

La Marea Roja stands at the south part of the stadium for 90 minutes every game, which attracts adults, women and large numbers of children.