Guaraní de Trinidad was founded on 12 October 1960 and joined the Liga Alto Paraná de Fútbol, a regional competition affiliated to the Unión del Fútbol del Interior (UFI) for football clubs from Hohenau and nearby districts such as Bella Vista, Jesús, Obligado, Pirapó and Trinidad.

They won the Liga Alto Paraná competition three times in a row between 2017 and 2019.

[1] The club entered the Campeonato Nacional B "Pre-Intermedia" (third tier competition organized by the UFI) for the first time in 2019, reaching the final where they defeated the team representing the Liga Carapegüeña (known as Sportivo Carapeguá in competitions organized by the Paraguayan Football Association) with a 4–2 aggregate score to earn direct promotion to the División Intermedia for the 2020 season.

Their relegation was confirmed on the last matchday of the tournament, with Guaraní losing 2–1 to Sportivo Luqueño.

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