Under the name Club Atlético Argentino de Rafaela, the club was founded in the city of Rafaela, Santa Fe Province in 1907 . In 1915 the name was changed to Club Atlético de Rafaela. The Monumental de Barrio Alberdi concrete stadium was erected in 1951.

The club was turned into a non-profit organization in 1988, and renamed Asociación Mutual Social y Deportiva Atlético de Rafaela ("Social and Sport Association Rafaela Athletic"). Only a year later Rafaela reached the second division after defeating Atlético Ledesma by 3-0.

Atlético de Rafaela played 14 years in the second division until the team won the Apertura2002 and the Clausura 2003 to finally reach first division. After losing the promociónagainst Huracán de Tres Arroyos, Atlético de Rafaela was relegated to the second division again.

The following season Atlético lost its chance to return to the first division, after losing thepromoción, against Argentinos Juniors.

In 2009 Rafaela earned another chance to return to the Primera División via a playoff against Gimnasia y Esgrima de La Plata. After winning the first final 3-0, Rafaela lost the second match by the same score (0-3), and had to stay in the second division once again.

Atlético de Rafaela fans are referred as Cremosos or Celestes, as well as the group of people that follows the team everywhere is known as La Barra de los Trapos .

The institution has also an important car racing circuit since 1919, which hosts many competitions including Turismo Carretera (since 1941) and TC 2000 (since 1983).

The 21st of May 2011, after defeating Atlético Tucumán by 2-0, they earned a spot back on the first division for the 2011-12 season.