The club was founded on 14 June 2020, based on the team representing the Pastoreo Sports League (Liga Deportiva de Pastoreo) in the Campeonato Nacional de Interligas, which won the competition in its 2019–20 edition after beating the team representing the Hernandarias league in the final. With this title the Pastoreo league earned the right to compete in the División Intermedia, however, in order to take part in competitions overseen by the Paraguayan Football Association such as the División Intermedia, teams promoted from the Campeonato Nacional de Interligas have to be refounded as clubs, causing the Liga de Pastoreo team to be refounded as Pastoreo Fútbol Club.[3]
Although they were entitled to enter the 2021 Paraguayan División Intermedia competition by having won the 2019–20 Interligas championship, the cancellation of the 2020 División Intermedia season due to the COVID-19 pandemic meant that they had their debut postponed to 2022 per decision by the APF's Executive Committee, since Guaraní de Trinidad (who were originally slated to have their debut in 2020) already held the berth reserved to the Unión del Fútbol del Interior (UFI) for that season as 2019 Primera B Nacional champions.[2] They eventually played the División Intermedia for the first time in 2022, ending the season in fourth place after being in contention for promotion to the top tier until the last rounds of the competition.[4]
Pastoreo competed in the División Intermedia until the 2025 season, in which the team placed fifth in the standings. However, they were relegated due to a poor campaign in the previous season that had an impact on the team's placement in the relegation table, which takes into account performances over the three most recent seasons. In that table, Pastoreo had 107 points in 90 matches, placing second-from-last and being relegated to the third tier as a result.[5]
