Founded as Costa Rica on 20 October 1948 by Manuel Guillén Fernández, the club joined the Costa Rican Third Division in 1949 and changed its name to Carmen Asociación Deportiva or just El Carmen de Alajuela a year later. They spent a few years in that league before reaching the second division in 1953 and on 9 April 1958 they debuted in the Primera División de Costa Rica against Alajuelense.
They won one championship in 1961, when the big clubs left the Federación Costarricense de Fútbol and founded their own ASOFUTBOL league and the title was contested between three club only: Carmen, Uruguay de Coronado and Gimnástica Española. However, the ASOFUTBOL teams returned to the league and their league winners Herediano were named champions only to recognize Carmen's title 40 years later.
From 1968 through 1975 they played in the third tier of the Costa Rican football pyramid again and from 1975 through 1991 they were in the second division except for one season in the top division in 1983. Renamed Carmelita, they won promotion to the Premier Division after Pérez Zeledón and Generaleña merged. In 2009 they dropped down again after 16 years in the Primera, only to bounce back again in summer 2012 after beating Orión in a promotion/relegation play-off.