The club was founded on 8 July 1901 by a group of students of the Colegio Nacional Ciencias del Cusco, the oldest school in Peru.

It has a large, longstanding rivalry with FBC Melgar of Arequipa known as El Clasico del Sur.

In 1966 Hector Ladrón de Guevara was the inaugural Cienciano player to be named captain of the Peru national team.

And in 1973, when Cienciano left the Cusco League and the Copa Peru behind to participate for the first time in the Peruvian First Division, it was understood that the authorities should no longer depend on the College for the attention that a competitive soccer team requires, which is why Waldo Callo, another of Cienciano's precursors, is stepping away from the presidency to make way for businessmen willing to invest and support the team.

Cienciano qualified for the 2002 Copa Libertadores for the first time and reached the Round of 16 but was eliminated by Club América of Mexico.

The team went through every later knockout round as the clear underdog defeating Peru's Alianza Lima in the Peru preliminary, Chile's Universidad Católica in the Chile-Peru Zone to enter the quarter-finals, Colombia's Atlético Nacional (once Copa Libertadores champion) in semi-finals and Brazil's Santos (twice Copa Libertadores champion) and in the quarter-final, to get to the finals.

[4] The game was played at Estadio Monumental de la UNSA in Arequipa (home of Cienciano's rivals Melgar, some of whose fans actually attended the match to root for River Plate) because of the insufficient capacity for a CONMEBOL final of the Estadio Garcilaso (which has been expanded since then in 2013).

The win was considered a severe upset because Cienciano had never been the Peru national champion (the team did win one half-year tournament in 2001 but lost the national championship title through a penalty shootout to the winner of the second tournament, Alianza Lima, in the year in which both celebrated their centenary.

The situation was repeated in 2006, but reversed: Cienciano won the second tournament but lost the final to Alianza Lima on aggregate.

As a result of winning the Recopa Sudamericana, Cienciano participated in the 2005 Copa Libertadores but were eliminated in the preliminary round to C.D.

In 2005, the Cusco-based club won the Torneo Apertura, but lost the superfinal to Sporting Cristal.

The following year, it won the 2006 Clausura, but lost the superfinal again to Alianza Lima, the same team that had beaten them in the 2001 national championship final.

After winning the 2006 Torneo Apertura, Cienciano qualified for the Copa Libertadores once again, but were eliminated in the group stage after placing last with four points.

In 2007, Cienciano qualified for the 2007 and 2008 Copa Libertadores after winning the 2006 Torneo Clausura and being the third placed team, and finished third in its group both editions.

Cienciano plays its home games in Estadio Garcilaso de la Vega which is in Centre of Cusco.

The stadium is known as the most beautiful in South America, with its seating in a rainbow and representing the colors of Cusco.

The initial renovation was meant to add a roof and modern wall around the stadium as well, but was not implemented due to a low budget.

[7] The largest ''barra'' or fan group is known as the La Furia Roja, The Red Fury.

It is the official fan group of Cienciano and is situated in the northern stand of the Estadio Garcilaso.

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