The club was founded under the name of Sport Alianza on 15 February 1901 by working-class youth in the Chacaritas neighborhood of Lima.

In 1987, tragedy struck Alianza when the entire squad and coaching staff died in an airplane crash as the team returned from an away fixture.

Alianza Lima has had a huge, long-standing rivalry with Universitario de Deportes, the most successful team in Peru with 27 titles, the match is known as the Peruvian Clásico.

The club was founded under the name of Sport Alianza on 15 February 1901 by working-class youth in the Chacaritas neighborhood of Lima.

Beginning in that first season, the colors of the Alianza stables, blue, white and black were used, and by the 1920s the classic vertically striped jersey had become the definitive kit.

Alianza participated in the amateur era of the Peruvian football league from that inaugural season, winning its first title in 1918.

The Alianza Stud changed owners and locations continuously and, consequently, the team was forced to relocate in turn, until 1928, when under the new name Alianza Lima, the club settled at the third block of the Manco Capac avenue in the La Victoria District, where it would stay and become the emotional home-base for club and fans alike.

This club which would later be renamed Universitario de Deportes and become Alianza's greatest rivals, in what is today the most important Peruvian derby.

The club won two Peruvian titles in a row in 1977 and 1978, when its players formed the majority of the Peru national football team.

The team had its greatest success at the international level in the 1976 and 1978 Copa Libertadores, in which managed to reach the semi-finals but lost to Deportivo Cali 1–4.

Then had one of its worst campaigns in 2007, until the 2010 edition, when they did a great campaign even defeating the defending champion Estudiantes de la Plata by 4–1 in Lima,[17] being one of the three top teams at the end of the first round however, in the Round of 16, they lost the chance to advance further with Universidad de Chile, after a controversial match in Chile,[18] where Ecuadorian referee Carlos Vera gave the Chilean side a goal that had already been flagged by the sideline referee as offside and the play had been called off, however Universidad de Chile's coaching staff including teammates and the pressure of a large local crowd seem to have given referee Carlos Vera the fast initiative to validate the goal, Alianza Lima had been eliminated in what Peruvian media and other South American media believed to be a robbery, Fox Sports network and ESPN agreed the play should not have been validated, Alianza Lima's president Guillermo Alarcon flew to Asuncion, Paraguay to speak to Conmebol and claiming a straight entry to the next Copa Libertadores, the case was also taken to FIFA headquarters but was not approved.

During the first years of the decade, despite having very good players, Alianza could not obtain titles, some which were snatched by Sporting Cristal, which was establishing itself as one of the three big football clubs of Peru.

The flight departed on 8 December in a Peruvian Navy Fokker F27 airplane, which crashed into the sea when it was a few kilometers away from the Lima-Callao Airport, close to the Ventanilla district in Callao.

The team had to restart from scratch and even former players who had already retired, like Teófilo Cubillas, or others who were about to, like César Cueto, played to help the club get out of these bitter times.

[23] In the early hours 2000, tragedy struck again when young captain Sandro Baylón died in a car accident after crashing with a post while driving under the influence of alcohol.

[25] Later on, Alianza Lima would win the 2003 and 2004 championships, defeating Sporting Cristal in both finals, this time under Argentinian manager Gustavo Costas.

In 2006 Alianza Lima again won the championship beating Cienciano del Cusco in the final play-off, enabling them to play the Copa Libertadores.

In 2017, Alianza Lima won its first championship in over a decade by winning both the Apertura and Clausura and, thus, did not require playing in the final playoffs.

At the end of 2020, Alianza was relegated to the second division,[26] despite the fact that in that year all games were played in just Lima and Callao because of the COVID-19 epidemic and teams from the provinces were not able to use their home stadiums.

Melgar beat Sporting Crystal 2–0 in each leg, coming out 4–0 winners on aggregate to set up a showdown with Alianza Lima for the 2022 Liga 1 title.

The first leg was played in Melgar's stadium in Arequipa and Alianza lost 1-0 due to a Yordi Vílchez own goal.

In 2023, defending champions Alianza lost to historic rivals Universitario de Deportes in the final, 3–1 on aggregate.

During the month of October, as a tribute to the Lord of Miracles, patron of the team, the regular colours are switched to purple and white.

[30] Alianza Lima plays its home games at the Estadio Alejandro Villanueva, also known as Matute for the neighbourhood it is located in.

[35][36] According to a survey carried out by the University of Lima, the Estadio Alejandro Villanueva is the most unsafe stadium in Peru to play football.

[37] Because of this, since 2016, the stadium has a video-monitoring center and is equipped with 50 high-tech security cameras located in different areas throughout, including both grandstands and the interior and exterior.

Alianza Lima's "Barra Brava", or Ultras group are called the Comando Svr (spelled with a "V" instead of a "U", intending to avoid the initial of bitter rivals Universitario).

[40] A survey of the Pontificia Universidad Catolica del Peru between November and December 2008 confirmed that Alianza is the most popular team with the 27% preference in Lima and Callao.

[41] A survey conducted by Ipsos support between 17 and 19 December 2008, Universitario ranked first in popularity with 34%, one percentage point below Alianza Lima with 33%.

Fans's loyalty to Alianza Lima cannot be matched in the continent, that it even surpassed other big soccer teams from Argentina and Brazil like Boca Juniors and Corinthians.