The team was created in 1919 when a group of friends that used to play in a team called the "Electra" at first and then "Once de Abril" (April the 11th) met at "Salon París". They wanted to give the city a team that could represent them at a national level. They played their first official game on August 2 of that same year against
Cartaginés getting their first victory, 3–1. , most important idol of the club. Alajuelense was part of the 7 teams that built and formed the National League in
Costa Rica, back in 1921, along with La Libertad,
Gimnástica Española,
Herediano,
Cartaginés, CS Tres Rios de La Union, and Sociedad Gimnástica Limonense. They won their first championship in 1928. They are the only team to win the championship with a perfect record; in 1941 they won all 6 games. In 1960, the team made a tour around the world, leaving Costa Rica on September 17. In 78 days, the team played 24 games, winning 12, losing seven and drawing five. They scored 71 goals and allowed 47, with a remarkable performance from Juan Ulloa Ramírez, the best player and top scorer of this tour. Alajuelense's best decade was the 1990s, during which they won 4 Championships and 4 sub-championships (2nd place finishes). By the end of the 1990's and into the middle of the 2000s, they won a total of 5 local championships, 2
Copa Interclubes UNCAF Trophies, and a
CONCACAF Club Championship. Alajuelense was the base for the Costa Rican football team in the Korea and Japan
2002 FIFA World Cup, fielding 9 players. By November 11, 2000, and after participating in the
Copa Merconorte, Alajuelense was ranked 27th in
IFFHS's Club World Ranking. It is the best rank any Central American club has reached. The club struggled with financial and administrative problems in the second part on the 2000s decade, so they decided to end contract with a lot of their regular and known players and started to build a team based on their younger divisions and make some structural changes. Nowadays the club is free of debts and with a team averaging 25-year-old players is still one of the best teams in the area and one of the teams with most fans in Costa Rica. On June 10, 2019, the club celebrated its 100th anniversary, being the second Costa Rican team to do so. In 2023, Alajuelense participated in the
2023 CONCACAF Central American Cup, and they would advance to quarter-finals after being leaders on the Group D. They would face
Cartaginés, that they would defeat 6–1 on aggregate, advancing to semifinals, where they would face
Herediano, defeating them 5–4 on penalties after a 4–4 aggregate draw. In the final, they would face
Real Estelí, but they would defeat them easily after a 4–1 victory on aggregate, being the first champions of the CONCACAF Central American Cup, and qualifying directly for the round of 16 of the
2024 CONCACAF Champions Cup. ==Stadium==