The club was founded in August 1924 under the name Federación Universitaria by students of the National University of San Marcos but was forced to rename in 1931.

[2] Since then, Universitario has won twenty-seven first division titles, and was the first Peruvian club, and the Pacific, to reach the final of the Copa Libertadores in 1972.

Once the season resumed, Universitario de Deportes reached the title after winning their last two games against Atlético Chalaco and Alianza Lima, 1–0 and 3–1 respectively.

The title drought of the fifties ended in 1959 when they won their eighth crown, after tying 3–3 with Deportivo Municipal in the final match, totaling fifteen wins, three draws and four losses.

On 19 April 1961, the club debuted in South America's premier competition in Montevideo, Uruguay against Peñarol, which ended in a loss of 5–0.

[42][43] In 1971, Universitario won its fourteenth First División title and qualified for the 1972 edition of the Copa Libertadores under the Uruguayan head coach Roberto Scarone along with Alianza Lima who placed second that season.

[53] Although Universitario lost, they had achieved something a Peruvian club had never before, reach the final of the Copa Libertadores, the most prestigious international competition in South America.

Universitario won the Torneo Regional, or Regional Tournament, of the early season successfully remained at the top of the league by advancing to the Liguilla by placing second in the Torneo Descentrlizado and conquering the Liguilla by winning all five matches played, the last of which was a 4–0 win over Los Espartanos de Pacasmayo with goals by Miguel Seminario, Fidel Suárez, Eduardo Rey Muñoz and Jaime Drago.

The defining derby was won by Universitario with a single goal by Fidel Suárez, overcoming the tie they had in the most Peruvian titles.

[59][60] In the year 1992, the national championship regulations were generally amended again by dropping the regional tournaments and returning to a similar system before the 1980s where the clubs would first play in a league and subsequently advance to the Liguilla.

The defining match that gave Universitario its twenty-first title was a 3–0 over San Agustín; two goals were scored by Jorge Amado Nunes and one by Roberto Martinez.

In 2002, Universitario beat Alianza Lima in the Apertura two-legged play-off but were unable to finish in the top four of the 2002 Clausura and were ineligible to dispute the national title.

In 2005, Universitario placed first on the aggregate table and qualified for the 2006 Copa Libertadores, where they won on away goals against Nacional in the first phase of the tournament, however, they were eliminated in the group stage.

They qualified for the 2009 Copa Libertadores but did not finish in the top seven of the Clausura and consequently could not contest the season final for the national title against Universidad San Martín.

[63][64] Much of the 2008 squad remained for the 2009 season, but with the departure of some notable players like Héctor Hurtado, Mayer Candelo and Donny Neyra.

[66] Other players to arrive were Carlos Orejuela, John Galliquio, Piero Alva, Francisco Bazán, Rodolfo Espinoza, and Ronaille Calheira.

A week later defeated by a score of 2–0 to Lanús and then tied 0–0 with Libertad, this meeting was the number 200 in the history of the club in the Copa Libertadores.

[71] Universitario ended his participation in the group stage with three more draws for a total of 10 points, and alongside Brazilian teams Internacional and São Paulo became the best defenders in the tournament to receive only two goals against.

[72] Coincidentally, the São Paulo was the merengue's rival in the knockout stage, both matches ended 0–0 so the winner was decided by penalty kicks resulting in the Brazilian club winning 3–1.

[75] The team quickly recovered with three straight wins[76] and not again suffer defeat until the twelfth journey when they lost by 1–0 before the León de Huánuco in visitor status.

[79] In the second stage championship of the "U" joined the league odd in which it scored 5 wins and 6 ties for a total of 72 points and obtain the qualification for the Copa Sudamericana 2011.

In the 2011 Peruvian Championship the team did not have a good start and it was only in the third round that they obtained their first victory; However, little by little, he began to raise his level and came to close his participation in the first phase at the top of the table.

During the second phase of the tournament, the club was saved from relegation in the penultimate round after drawing 2–2 with Universidad César Vallejo at the Estadio Nacional.

[80] At the international level, the club showed a different face and for the first time in its history advanced to the quarterfinals of the Copa Sudamericana where they were eliminated by Vasco da Gama from Brazil by an aggregate score of 5–4.

[82] With this measure, the board of directors was disintegrated and Rocío Chávez Pimentel, president of Right Business S.A., was appointed temporary administrator of the club.

[83] In 2024, "la U" celebrated its 100th anniversary since being founded,[84][85] and also won the Apertura and Clausura tournaments played in the season to claim its 28th league title.

Alianza's fans, in the southern stand, reacted violently to the loss by vandalizing the premises and causing two reported stabbings.

[91] Consequently, La U was forced to play all future derbies at Estadio Nacional where the Instituto Peruano del Deporte installed artificial turf which is constantly criticized by the First Division players.

Many saw this as a typical bullying behavior on the part of the president since this stadium would have been the perfect venue to host the 2004 Copa América intro as well as final games.

Trinchera Norte is a barra brava that was formed in 1988; in contrast to Alianza Lima's supporters, named "Comando Svr", "Sicarios", and others.