Founded on 12 October 1932 as an honour to military leader Martín Miguel de Güemes,[1] the club mainly played in regional competitions.

In 1986, after winning the previous year's Torneo Regional, they featured in the 1986 Liguilla Pre-Libertadores, being knocked out by Ferro Carril Oeste in the qualifying rounds.

Güemes narrowly missed out on promotion to Primera B Nacional in 1988; after leading their zone in the Torneo del Interior, the club reached the finals but lost to San Martín de Tucumán.

[3] On 28 December 2015, Güemes defeated San Martín de Formosa and reached the Torneo Federal A for the first time in their history.

[4] Despite suffering immediate relegation,[5] the club returned to the division for the 2019–20 campaign,[6] where they led their group before the season was curtailed due to the COVID-19 pandemic.