The club was founded on 7 April 2018 based on the team representing the Liga Atyreña de Deportes in the Campeonato Nacional de Interligas, the third tier competition for regional leagues affiliated to the Unión del Fútbol del Interior (UFI).

[3] Since league teams promoted from the Campeonato Nacional de Interligas have to be refounded as clubs in order to take part in competitions overseen by the Paraguayan Football Association such as the División Intermedia, the Liga Atyreña team was refounded as Atyrá Fútbol Club.

For their first campaign in the División Intermedia, Atyrá hired the former Paraguayan footballer Ángel Martínez Rotela as manager.

[5] Atyrá's performance in their first participation in the División Intermedia was consistent, however they fell short of reaching promotion to the Paraguayan Primera División as they finished the season in fourth place with 49 points, trailing the eventually promoted sides Guaireña and 12 de Octubre by eight and seven points, respectively.

[6] The club plays its home matches at Estadio San Francisco de Asís in Atyrá, which has a capacity of 10,000 spectators.