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Founded 3 January 1936, they were named after the first FIFA World Cup champions, Uruguay. They changed their first club colors, red and black like Alajuelense, to the yellow and black of Uruguayan giants Peñarol and made their Primera División debut in 1950. In 1961, they became runner-up to champions El Carmen, when the big clubs left the Federación Costarricense de Fútbol and founded their own ASOFUTBOL league and the title was contested between three clubs only: Carmen, Uruguay de Coronado and Gimnástica Española. However, the ASOFUTBOL teams returned to the league and only Uruguay retained their place in the top tier.

In 1963, they surprisingly won the league with players like "Caballo" Otárola, "Camarón" Padilla, Luis Chacón, Carlos Luis "Piche" García and Rodrigo "Riguín" Sandoval.

They played in the Primera División from 1988 until relegation in 1992. Uruguay returned to the top flight in summer 2012.