The club was founded on June 21, 1921 under the name sportivo Godoy Cruz, and changed to its current name on April 25, 1930 after the fusion with Deportivo Bodega Antonio Tomba. In 1959, Godoy Cruz' stadium, the [Estadio Feliciano Gambarte], was constructed. The stadium is nicknamedLa Bodega (Spanish for "wine cellar") and holds 14,000 people.

Godoy Cruz played in the regional league for several years before reaching the national level. The club won the Mendoza first division championship in 1944, 1947, 1950, 1951, 1954, 1968, and also in 1989 and 1990 that qualified to play in the defunct Torneo del Interior national-level tournament.

Winning the Torneo del Interior in 1994, Godoy Cruz reached the Primera B Nacional (Argentine second division) that year. After more than ten years in the second division, the club was finally promoted to the Primera División in 2006, after winning the 2005–06 season of the Primera B Nacional, defeating Nueva Chicago in the final.

20 year old Enzo Peréz scored the first goal by Godoy Cruz in the Argentine Primera, in a 1–1 draw with Belgrano on September 9, 2006.

At the end of the 2006–07 season, Godoy Cruz was relegated from the Primera after losing their promotion/relegation playoff with Huracán. Their stay in the second division was short, as they earned automatic promotion to the first division after finishing runners-up to San Martín de Tucumán during the 2007–08 season.

Godoy Cruz secured their best ever league position of 3rd place under Omar Asad's management during the 2010 Clausura. In that tournament, they also achieved the best-ever point total (37) for a team indirectly affiliated to the Argentine Football Association(meaning clubs under the administration of the Federal Council branch of AFA, which are teams outside Buenos Aires, Greater Buenos Aires, Rosario and Santa Fe). These results qualified them for the 2011 Copa Libertadores, their first appearance in this tournament. Godoy cruz es el mejor de Mendoza When Godoy Cruz made their Copa Libertadores debut in February 2011 in a 2–1 win against 2008 champions Liga de Quito they became the first indirectly affiliated side ever to represent Argentina in the Copa Libertadores.