UES

Universidad was founded in 1956. They slowly progressed up from the third division up until the Liga de Ascenso (Segunda División) where they remained there for six years.

Universidad was promoted to El Salvador's first division football league (Liga Mayor A) in the 1963–64 season. One of the key signings was that of 18-year-old Mauricio "Pipo" Rodríguez, a slender footballer with a knack for scoring spectacular goals, having considerable power with either leg. He would become the club's most influential player, even to this day.

The club's first season back was not successful at all. In that 1963–64 season, Universidad barely staved off relegation by a single point over Dragón which had managed a mere 14 points. The following season, the club had a more respectable run where it climbed to the middle of the table; however goals were hard to come by, having scored only 18 in as many games.

The 1965–66 season remains by many the most successful in the team's history. During this time, the format of El Salvador's first division changed, 4 rounds were played (36 games) instead of the customary 2 (18 games). It was during this campaign that CD Universidad was transformed. Led by "Pipo" Rodríguez, the squad became an all out attacking unit, displaying the flair that captured many of the neutral fan's attention.

However, their attacking flair (69 goals) was more than matched by Alianza, which finished top of the table with 50 points, 3 ahead of Universidad. "Pipo" Rodríguez finished as top scorer with 23 goals (tied with Alianza's Cascarita Tapia). One of the key moments occurred in the tail end of the season when CD Universidad traveled to California, United States to play a couple of exhibition matches with only 3 games left in the campaign. Later that same week, Universidad arrived back in El Salvador to play against an Once Municipal team fighting relegation. Tired Universidad players could not cope and lost the game.

For the rest of the decade Universidad, in spite of their attractive style, languished in the middle of the table finishing 6th, 7th and 8th respectively.

The 1970 season saw another mid table finish for Universidad. However, in spite of their unassuming 6th-place finish, their 63 goals scored were fourth most in the first division and the team finished only 6 points behind eventual winner Atlético Marte, in what was one of the tightest races in the history of El Salvador's Liga A. The team closed the season with an impressive unbeaten streak in their last round to propel themselves as one of the teams to content for the league championship the following campaign.

Universidad were a serious contender in the 1971 season. The team, reinforced with the names of Gualberto Fernández in goal, Argentine striker Joaquin Cazalbón and Cascarita Tapia finished third in the league, 5 points behind eventual winners Juventud Olímpica and a single point behind Alianza. Universidad and Alianza interchanged leadership of the table for the majority of the first two rounds; however, Juventud Olímpica joined the race in the third round and didn't falter. At the end of the season, it was a 3-way tie between the 3 clubs with 44 points and only a 2 matches remaining in the schedule. Universidad had played one more match than Juventud Olímpica and needed a win when they met the co-leaders on 25 November 1971. Unfortunately, a 4-minute goal by Moises Gonzalez gave the "academia de oro" the victory which left a deflated "U" without the league title. Juventud Olímpica went on to defeat Alianza (1–0) in the last match of the season to earn their first league title. Universidad's inability to record victories against minnows such as Excelsior and Adler cost them dearly, as well as blowing 3–0 and 2–0 leads against Atletico Marte in the course of the campaign. Universidad's third-place finish at least allowed them to complete in the second Confraternidad tournament.

The format changed, yet again in 1972, which would be the last campaign for the gifted "Pipo" Rodríguez. Injuries had taken their final toll on his knees and ankles which led to his premature retirement at the age of 27 years. The new format called for 2 rounds (18 games) and thereafter, the top six teams would battle for the championship on a home-away round-robin format (10 games). Universidad managed to qualify, finishing in a very modest 5th place and scoring only 18 goals; however, in the "Liguilla" Universidad's attacking prowess came to the front (scoring 15 goals – tops in the "Liguilla") and, ranked as outsiders to win the championship, were the last team to have a chance of overtaking Águila for the championship. Universidad lost their last game 1–2 against FAS, while Águila defeated Municipal Limeño 1–0 to become champions.

The 1973 season was a restart of sorts as the main-stay of "Pipo" Rodríguez would no longer appear in the team's lineup. His absence was also manifested in the field of play as Universidad finished in fifth place after 2 rounds and just managed to qualify for the "Liguilla". However, unlike the previous season, Universidad only managed a paltry 3 points from 10 games and did not record a single win. Their dispirited play was quite evident in their 2 games against Atlético Marte, where they were soundly beaten 3–0 and 1–0.

The 1974–75 season held a lot of promise as "Pipo" Rodríguez returned to manage the team. Two Argentines of high quality bolstered the team, central attacker Tony Rojas, who scored with headers as much as with his feet and Victor Donato, a long blonde haired technician, who became the creative conduit of the team in midfield. Tomás "Flaco" Pineda returned to CD Universidad after a successful spell with Juventud Olímpica and replaced René Puquirre in goal. With other national footballers such as Victor "El Pato" Valencia, Eduardo "La Guapa" González, Celso Jurado, Mauricio "Chino" Quintanilla and Wilfredo Peñate, Universidad had an outstanding team that could vie for the championship. In addition, "Pipo" Rodríguez also brought an 18-year-old footballer who would become one of El Salvador's most talented players of all time, Norberto "Pajarito" Huezo.

It all started well, when prior to the season, Universidad won the "Torneo Relámpago", a mini tournament which consisted of the 10 teams in first division playing 10-minute games against each other on a knockout format. In the absence of goals, corners or shots on goal determined the winner.

In spite of an inaugural 1–1 tie against perennial powers Águila, Universidad quickly climbed to the top of the table by winning their next 6 games. Important wins against newly promoted Platense (1–0) – a side that would become champions, Atlético Marte (4–1), Negocios Internacionales (3–1), Alianza (1–0) and FAS (1–0) in the first round laid out their intentions. However, after remaining unbeaten in their first 11 games (8 wins and 3 ties), injuries to key players such as "Flaco" Pineda and Tony Rojas, which kept them on the sidelines throughout most of the second half of the season, slowed Universidad's progress and their faltering form saw them miss out of the play-offs to Platense and Atlético Marte. The format had again changed to 4 rounds (36 games) with the top 4 teams staging a semi-final play-off before advancing to the final.

There were few significant changes for the 1975–76 season. Tomas "El Flaco" Pineda departed to Luis Ángel Firpo leaving Juan "Gatti" Méndez (acquired from Municipal Limeño) in charge of goal. Norberto "Pajarito" Huezo and Victor "El Pato" Valencia now played for ANTEL and Alianza, respectively. Mauricio "Chino" Quintanilla had matured into the team's main attacking threat alongside the talented Tony Rojas. During this season, Universidad stayed atop the table throughout the entire season. The format had changed again where the season consisted of 3 rounds where teams where divided into two groups of six teams (33 games – 12 teams) with the top 2 teams from each group qualifying for the semi-finals. Universidad recorded several impressive results, defeating FAS and Atlético Marte 1–0, Sonsonate 4–0 and the highlight of their season, a comprehensive 2–0 victory over Águila over a rainy "Flor Blanca" field in the second round, with Victor Donato majestically exerting his influence in midfield.

At the end of the season, "La U" finished in 2nd place of their group with 40 points (1-point behind Alianza; 2 points ahead of Sonsonate) and qualified for the play-offs against a top seeded and record setting Águila team which had scored an impressive 79 goals during the season, 24 more goals than its nearest competitor. Universidad went into the first leg of the semi-final game as rank outsiders, in spite of having beaten Águila 2–0 in the second round, they had lost 0–4 and 0–2 in the first and third round respectively. Universidad confounded critics and fans alike by producing a masterclass performance and besting Águila by a score of 3–1; this in spite of missing a penalty when the score was still tied 0–0. The victory afforded "La U" the luxury losing the 2nd leg (by no more than 1 goal) and still qualify for the final. However, in the return match, Universidad was a mere shadow of the team that had previously dismantled Águila and allowed their opponents complete control of midfield. The 0–3 half-time deficit was reflective of their display and even after scoring in the 2nd half to make the game 1–4, Águila cemented their place in the final with another goal to end the game at 1–5 with a 6–4 aggregate score. Universidad played against FAS for 3rd/4th place devoid of foreign footballers and managed a respectable 1–1 half-time score before losing 1–4.

For the remainder of the decade, Universidad cut back on reinforcements (Tony Rojas, Victor Donato, Juan Méndez, Roy Saénz all left the team) due to limited financial resources and was constantly battling relegation, finishing in 11th, 9th, 10th place, when finally, during the 1979–80 season, was relegated to the second division (Liga B).

From the next four seasons Universidad remained on the lower half of the table often escaping relegation on the last few games of the season, eventually, however, UES fell to relegation on 21 December 1986 after a dismal season futboldelsalvador.com. The club fortunes continued to decline struggling on the field (leading them to be relegated down to the third division) and financially, which almost lead the club to merger with Metapán FC in 1992. UES spent almost 11 years in the Tercera División before purchasing Real Santa Ana FC spot in the Segunda División (2002–03 season), however after a dismissal season the club was once relegated back to the Tercera División. It took another five years before UES were able to gain promotion in May 2008.

UES qualified for the final series of the Clausura 2010 tournament of the Segunda División. After eliminating El Roble, they defeated the highly fancied Once Municipal over two legs 3–1 in the semi-finals, before they went on to defeat Fuerte Aguilares 3–1 in the grand final and being crowned champion of the 2010 Clausura on 2 June 2010 at the Estadio Cuscatlán.futboldelsalvador.com Thanks to winning the 2010 Clausura, it gave them an opportunity to face 2009 Apertura champion Once Municipal for the only spot to be promoted to the first division. On 6 June 2010, at the Estadio Jorge "Mágico" González UES defeated Once Municipal 2–1 thanks to goals from Williams González on the 72 min and the extra time winner by Henry Pérez on the 109 min.

C.D. Universidad de El Salvador, after a long battle in the season against Dragón, succumbed again to the relegation during the 2017 Clausura tournament. Efrain Burgos led the team during the entire championship, achieving in the first months good progress and excellent results to save the team from the relegation. However, almost at the end of the championship, the team began to fail in decisive matches, in an inexplicable way.

Two away defeats in a row against Águila (2–3) and Alianza (0–2) at the Estadio Cuscatlán, put the team in a very compromised situation in the relegation battle. A victory against Luis Ángel Firpo (2–1) at the Estadio Universitario gave limited hope for the team. The relegated team was decided in the last day of the national league, with all games played at the same time, C.D. UES were winning against Pasaquina (1–0) at the Estadio Universitario, but, in the final minutes, Dragón beat his biggest rival in the national league, Águila (0–1, in the Estadio Cuscatlán), condemning C.D. UES to the relegation zone, in one of the most exciting non-relegation finals of the national league.

With the relegation already assumed, bureaucratic problems prevented the team from being registered in the Segunda División de El Salvador, generating a collapse of the team that generated serious administrative problems with the authorities of "La Liga de Plata". The non-payment to players (situation that days later was solved) only brought more problems to the team. Finally, by not being enrolled in Second Division, and by not generating economic income, and also for the lack of interest of the university sports authorities in keeping the club competing, the club finally disappeared in 2017.

In July 2018, CD UES it was restructured as a professional football team. Now CD UES compete in the Tercera Division de Fútbol Salvadoreño for the Apertura 2018 tournament. The team emerges again after many administrative and bureaucratic problems, being led by national coach and former UES player Santiago Iraheta in the project at the Tercera División. The team is composed mostly of students of the Universidad de El Salvador also highlighting some experienced players like Sergio Calero and Javier Durán, who were part of the youth reserves of CD UES in the Primera División.

On the return to the Estadio Universitario UES played before a friendly match against Saprissa FC of Chalatenango (5–0 victory). UES was put in the Grupo Oriente A, and his first official match was a 2–3 defeat against Altético San Lorenzo. UES first home match was a 3–2 victory against Maracaná de San Rafael.

In the Estadio Universitario the team has kept his unbeaten streak as November 2018, including the team's debut at the Copa El Salvador after a 2–1 victory against El Vencedor, club of the Segunda División. The biggest victory of CD UES to date it was a 7–1 victory against AD La Herradura.

UES secured the third place in their group and faced CD Gerardo Barrios for the quarter-finals. In the first leg UES achieved a 2–1 victory in the Estadio Universitario. But in the second leg, UES lost 1–3.

In July 2021, the university committee unanimously decided to not sign for 2021 third division due to the ever rising cost due to the COVID-19 pandemic. The club has not participated in any division since.