Although the current Juan Aurich has played for only a few years in the top-flight, three other football clubs named Juan Aurich have played in the Torneo Descentralizado. The first Juan Aurich was founded in 1922 and played in the first division between 1967 and 1983 and again between 1988 and 1991. Between 1994 and 1996 the merged football club Aurich–Cañaña had a brief spell in the Primera División after they achieved promotion through the 1993 Copa Perú. Finally, a third Juan Aurich football club achieved promotion in 1997 by winning the 1997 Copa Perú. This spell in the first division lasted from 1998 to 2002.
The club's first major success was won in 2007 with the promotion to the Primera División via the Copa Perú. Four years later they conquered their second major success after winning the 2011 Torneo Descentralizado, defeating Alianza Lima in the third leg of the finals in a penalty shootout.
The first incarnation of the football club was founded by a group of workers of the hacienda Batán Grande on 3 September 1922 as Club Deportivo Juan Aurich, after the owner of the hacienda, Juan Aurich Pastor. The club played two spells in the first division, the first between 1967 and 1983 and the second between 1988 and 1991. Following their relegation at the end of the 1991 Torneo Descentralizado, a new football club was formed, albeit a merge, between the remaining Juan Aurich club and Deportivo Cañaña. This merged club—led by manager Horacioa Baldessari—won the 1993 Copa Perú and gained promotion. They held a brief spell between 1994 and 1996 until their relegation at the end of the 1996 season. A new reincarnation of Juan Aurich was formed as Juan Aurich de Chiclayo shortly after Aurich–Cañaña was relegated. The new Juan Aurich achieved promotion through the 1997 Copa Perú and played from 1998 until 2002 when they were relegated. Due to the financial strain created by playing in the top flight, Juan Aurich de Chiclayo also folded as its predecessors.
In November 2004, Juan Merino Aurich took control of the waning football club Mariscal Nieto of the La Victoria district of the Chiclayo Province. Merino converted the club to Juan Aurich de La Victoria and founded the current incarnation of Juan Aurich on 28 January 2005. In 2006, they finished first in the regional stage of the 2006 Copa Perú advanced to the national stage of the tournament. They overcame their rivals in the Round of 16 and the quarter-finals but fell to Hijos de Acosvinchos in the semifinals. The following season they again reached the regional stage of the 2007 Copa Perú and finished first. This time, however, they achieved promotion to the 2008 Torneo Descentralizado by advancing to and winning the finals. Baldessari, as in 1993, led the team and defeated Sport Águila in the finals in a penalty shootout.
Their first season in the first division was not remarkable. In the Torneo Apertura, they finished eighth and in the Torneo Clausura they finished twelfth. Consequently, the club finished twelfth on the aggregate table and tied on points with Atlético Minero, which finished thirteenth. The two teams played an extra match to determine the relegated team. Juan Aurich defeated Atlético Minero 2–1 and remained in the first division.