Beginnings Cienciano was founded on 8 July 1901 by a group of students from the National School of Science of Cusco (
Colegio Nacional Ciencias del Cusco). It participated in several leagues and tournaments of the region. They played their first official match on 27 July 1902 against Atletic Club in Cusco. Cienciano soon won its first trophy, winning the 1903 Liga Departamental del Cusco, and would go on to win it 27 times from 1912 to 1983.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. The Cienciano team was managed by the teachers of the Cienciano Alma Mater School until the mid-sixties, when after the creation of the
Copa Perú, football in Peru became more competitive. 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 remained in the First Division until 1977, where they were relegated to the
Peruvian Second Division. 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. Since then, the club has always played in the First Division.
The Golden age (2000–2007) First League title In 2001, Cienciano celebrated its 100 year anniversary by winning its first title with the
2001 Torneo Clausura of the
Peruvian Primera División, although it lost the superfinal (played between the winners of the Apertura and Clausura tournaments) to
Alianza Lima. 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.
Copa Sudamericana win in 2001 In 2003, Cienciano, led by Peruvian coach
Freddy Ternero, qualified to the
Copa Sudamericana for the first time in its history, after beating
Sporting Cristal in an internal qualifying tournament. 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. Once at the finals the team faced one of the biggest teams in South American football, River Plate of
Argentina (twice Copa Libertadores champion). After a 3–3 draw in
Buenos Aires, Cienciano went on to win 1–0 in Peru with a free-kick goal by Paraguayan defender
Carlos Lugo, which put the aggregate score at 4–3 in its favor to win the final. 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). As a result to winning the Copa Sudamericana, Cienciano qualified for the Copa Libertadores but lost to
C.D. Guadalajara of Mexico in the qualifying round, 8–2 on aggregate. 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, which was in the
Copa Libertadores (
Universitario in 1972 and
Sporting Cristal in 1997). Both teams were defeated in the finals. 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.
Recopa Sudamericana win 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 the
UEFA Super Cup, which was disputed between the winners 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 4–2 on penalties. The match was played at
Lockhart Stadium in
Fort Lauderdale, Florida. Soon after the club's win in the Recopa Sudamericana, the
Guatemala national football team organized a friendly against the club. Cienciano won the friendly three goals to zero. 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. Guadalajara of Mexico.
More league titles and superfinal runner-ups 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. A year later, they qualified again for the Copa Sudamericana but were eliminated in the Round of 16. Since then, Cienciano has not qualified for the Copa Libertadores.
Relegation and comeback In
2015, the club was relegated after finishing in the bottom three of the aggregate table. The club finished third and was one point off from the title play-off in the
2016 season. In
2018, the club won third place in the league and participated in the promotion play off group, where the top two teams get promoted to the
2019 Liga 1. Cienciano placed third with four points. In 2019, it was finally promoted back to the first division after winning the
2019 Liga 2, winning their first national competition. After the
2021,
2022 Liga 1 seasons, Cienciano qualified for the
2022 and
2023 Copa Sudamericana after placing in the top 8 of the league. The club was eliminated in the first stage in both editions. In 2025, the club qualified for the
2025 Copa Sudamericana group stage. == Kit and crest ==