Cienciano was founded in 1901 by a group of students from the NationalSchool of Science of Cusco. It participated in several leagues and tournaments of the region. In 1966 Hector Ladrón de Guevara was the inaugural Cienciano player to be named captain of the Peru national team. In 1972, it began to play in the Peruvian First Division. However, the club was relegated four years later. In 1988, the FPF invited the club to play in a tournament of the southern region. In 1991, Cienciano won the tournament and in 1992 it once again played in the First Division. Although the club came close to relegation in 1994, the team remains in the First Division.
In 2003 Cienciano, led by their coach Freddy Ternero, made it for the first time to the Copa Sudamericana, after beating the current Peruvian champion Sporting Cristal in an internal qualifying tournament. It went through every later knockout round arguably as the underdog defeating Peru's Alianza Lima, Chile's Universidad Católica, Colombia's Atlético Nacional and Brazil's Santos, to get to the finals. Once at the finals they faced one of the biggest teams in South Americanfootball, River Plate of Argentina. After a 3–3 draw in Buenos Aires, Cienciano went on to win 1–0 on their home game in Peru with a goal from a free kick by Paraguayan defender Carlos Lugo. The game was played in Arequipa because of the insufficient capacity for a CONMEBOL final of the Estadio Garcilaso. This was the first international championship for a Peruvian team in history, only two other Peruvian teams had advanced to the finals of an international tournament, the Copa Libertadores and was defeated. However, Cienciano had never won the Peru national champion.
After winning the Copa Sudamericana, Cienciano went on to play against Boca Juniors of Argentina, another South American giant, for the 2004 Recopa Sudamericana, this being just one match, much like UEFA's European Super Cup, that faced the winner of both South American Cups of the previous season: the Copa Sudamericana and the Copa Libertadores. After a 1–1 draw, Cienciano went on to win the title by penalty shootout. The match was played in Fort Lauderdale, Florida.
Cienciano play their home games in Estadio Garcilaso de la Vega which is in Cusco. It was named after the Peruvian Inca Garcilaso de la Vega. When first inaugurated in 1950, it had a spectator capacity of 22,000 and had a running track. In 2004, the stadium's capacity was expanded to 42,000, losing its running track, because of Cienciano's success in international tournaments and it would be a venue in the 2004 Copa América. Cienciano shares the stadium with city rivals Deportivo Garcilaso and Cusco FC.
